From julien.jourde at pasteur.fr Fri Feb 1 14:09:07 2013 From: julien.jourde at pasteur.fr (Julien Jourde) Date: Fri, 01 Feb 2013 15:09:07 +0100 Subject: [ome-users] insight.jnlp and Nginx redirection Message-ID: <510BCC83.3060009@pasteur.fr> Hi Omero-users, I just installed a 4.4.5 omero server in my lab. Everything's fine except when I try to launch Insight using the jnlp protocol. The problem seems to come from the redirection of the port 80 to the port 443 in nginx. I'm using "rewrite ^ https://$server_name$request_uri? permanent;" in my omero.conf file to accomplish that. But the jnlp file can't deal with that. It contains urls like "http://my.omero.server.fr/webstart/jars/insight.jnlp" where it shoud be "https://my....". Launching the jnlp leads to a launchfile error because it tries to charge a web page unproperly created by nginx (see below). Did I made something wrong by using redirection rules ? Is there a way to do it more properly ? Thanks for your help :) Julien PS : the nginx redirection page with a

missing tag : 301 Moved Permanently

301 Moved Permanently

nginx/1.0.15 From nikolaus.ehrenfeuchter at unibas.ch Fri Feb 1 14:12:01 2013 From: nikolaus.ehrenfeuchter at unibas.ch (Niko Ehrenfeuchter) Date: Fri, 01 Feb 2013 15:12:01 +0100 Subject: [ome-users] insight.jnlp and Nginx redirection In-Reply-To: <510BCC83.3060009@pasteur.fr> References: <510BCC83.3060009@pasteur.fr> Message-ID: <510BCD31.5000001@unibas.ch> On 01.02.2013 15:09, Julien Jourde wrote: > Hi Omero-users, > > I just installed a 4.4.5 omero server in my lab. Everything's fine > except when I try to launch Insight using the jnlp protocol. > > The problem seems to come from the redirection of the port 80 to the > port 443 in nginx. > > I'm using "rewrite ^ https://$server_name$request_uri? permanent;" in my > omero.conf file to accomplish that. But the jnlp file can't deal with > that. It contains urls like > "http://my.omero.server.fr/webstart/jars/insight.jnlp" where it shoud be > "https://my....". Launching the jnlp leads to a launchfile error because > it tries to charge a web page unproperly created by nginx (see below). > > Did I made something wrong by using redirection rules ? Is there a way > to do it more properly ? we experienced exactly the same problem here - I'll go and ask the person who fixed it (or created a workaround, can't remember that) what he did. Cheers Niko From nikolaus.ehrenfeuchter at unibas.ch Fri Feb 1 14:20:41 2013 From: nikolaus.ehrenfeuchter at unibas.ch (Niko Ehrenfeuchter) Date: Fri, 01 Feb 2013 15:20:41 +0100 Subject: [ome-users] insight.jnlp and Nginx redirection In-Reply-To: <510BCD31.5000001@unibas.ch> References: <510BCC83.3060009@pasteur.fr> <510BCD31.5000001@unibas.ch> Message-ID: <510BCF39.3030400@unibas.ch> On 01.02.2013 15:12, Niko Ehrenfeuchter wrote: > On 01.02.2013 15:09, Julien Jourde wrote: >> Hi Omero-users, >> >> I just installed a 4.4.5 omero server in my lab. Everything's fine >> except when I try to launch Insight using the jnlp protocol. >> >> The problem seems to come from the redirection of the port 80 to the >> port 443 in nginx. >> >> I'm using "rewrite ^ https://$server_name$request_uri? permanent;" in my >> omero.conf file to accomplish that. But the jnlp file can't deal with >> that. It contains urls like >> "http://my.omero.server.fr/webstart/jars/insight.jnlp" where it shoud be >> "https://my....". Launching the jnlp leads to a launchfile error because >> it tries to charge a web page unproperly created by nginx (see below). >> >> Did I made something wrong by using redirection rules ? Is there a way >> to do it more properly ? apparently we do have an exception for webstart in the rewrite rules: > if ( $uri !~ ^/webstart/jars/insight.jnlp ) { > rewrite ^ https://$server_name$request_uri? last; > } This workaround seems to get things going here, but anyway I think the hardcoded "http" in the jnlp file should rather get fixed. Cheers Niko From julien.jourde at pasteur.fr Fri Feb 1 14:42:58 2013 From: julien.jourde at pasteur.fr (Julien Jourde) Date: Fri, 01 Feb 2013 15:42:58 +0100 Subject: [ome-users] insight.jnlp and Nginx redirection In-Reply-To: <510BCF39.3030400@unibas.ch> References: <510BCC83.3060009@pasteur.fr> <510BCD31.5000001@unibas.ch> <510BCF39.3030400@unibas.ch> Message-ID: <510BD472.7070004@pasteur.fr> Le 01/02/13 15:20, Niko Ehrenfeuchter a ?crit : > On 01.02.2013 15:12, Niko Ehrenfeuchter wrote: >> On 01.02.2013 15:09, Julien Jourde wrote: >>> Hi Omero-users, >>> >>> I just installed a 4.4.5 omero server in my lab. Everything's fine >>> except when I try to launch Insight using the jnlp protocol. >>> >>> The problem seems to come from the redirection of the port 80 to the >>> port 443 in nginx. >>> >>> I'm using "rewrite ^ https://$server_name$request_uri? permanent;" >>> in my >>> omero.conf file to accomplish that. But the jnlp file can't deal with >>> that. It contains urls like >>> "http://my.omero.server.fr/webstart/jars/insight.jnlp" where it >>> shoud be >>> "https://my....". Launching the jnlp leads to a launchfile error >>> because >>> it tries to charge a web page unproperly created by nginx (see below). >>> >>> Did I made something wrong by using redirection rules ? Is there a way >>> to do it more properly ? > > apparently we do have an exception for webstart in the rewrite rules: > >> if ( $uri !~ ^/webstart/jars/insight.jnlp ) { >> rewrite ^ https://$server_name$request_uri? last; >> } > > This workaround seems to get things going here, but anyway I think the > hardcoded "http" in the jnlp file should rather get fixed. > > Cheers > Niko Thanks a lot for your answer. I'll try your solution. Hope it works ! Cheers JJ From will at lifesci.dundee.ac.uk Fri Feb 1 15:51:13 2013 From: will at lifesci.dundee.ac.uk (Will Moore) Date: Fri, 1 Feb 2013 15:51:13 +0000 Subject: [ome-users] insight.jnlp and Nginx redirection In-Reply-To: <510BCF39.3030400@unibas.ch> References: <510BCC83.3060009@pasteur.fr> <510BCD31.5000001@unibas.ch> <510BCF39.3030400@unibas.ch> Message-ID: <85AB7FB5-B30A-49D1-AAB6-A1063A554E00@lifesci.dundee.ac.uk> Hi Julien and Niko, Thanks for your feedback and input. I have created a ticket for this issue: https://trac.openmicroscopy.org.uk/ome/ticket/10273 Cheers, Will. On 1 Feb 2013, at 14:20, Niko Ehrenfeuchter wrote: > On 01.02.2013 15:12, Niko Ehrenfeuchter wrote: >> On 01.02.2013 15:09, Julien Jourde wrote: >>> Hi Omero-users, >>> >>> I just installed a 4.4.5 omero server in my lab. Everything's fine >>> except when I try to launch Insight using the jnlp protocol. >>> >>> The problem seems to come from the redirection of the port 80 to the >>> port 443 in nginx. >>> >>> I'm using "rewrite ^ https://$server_name$request_uri? permanent;" in my >>> omero.conf file to accomplish that. But the jnlp file can't deal with >>> that. It contains urls like >>> "http://my.omero.server.fr/webstart/jars/insight.jnlp" where it shoud be >>> "https://my....". Launching the jnlp leads to a launchfile error because >>> it tries to charge a web page unproperly created by nginx (see below). >>> >>> Did I made something wrong by using redirection rules ? Is there a way >>> to do it more properly ? > > apparently we do have an exception for webstart in the rewrite rules: > >> if ( $uri !~ ^/webstart/jars/insight.jnlp ) { >> rewrite ^ https://$server_name$request_uri? last; >> } > > This workaround seems to get things going here, but anyway I think the hardcoded "http" in the jnlp file should rather get fixed. > > Cheers > Niko > _______________________________________________ > ome-users mailing list > ome-users at lists.openmicroscopy.org.uk > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.woodbridge at imperial.ac.uk Mon Feb 4 09:29:25 2013 From: m.woodbridge at imperial.ac.uk (Mark Woodbridge) Date: Mon, 4 Feb 2013 09:29:25 +0000 Subject: [ome-users] insight.jnlp and Nginx redirection In-Reply-To: <85AB7FB5-B30A-49D1-AAB6-A1063A554E00@lifesci.dundee.ac.uk> References: <510BCC83.3060009@pasteur.fr> <510BCD31.5000001@unibas.ch> <510BCF39.3030400@unibas.ch> <85AB7FB5-B30A-49D1-AAB6-A1063A554E00@lifesci.dundee.ac.uk> Message-ID: <510F7F75.6030602@imperial.ac.uk> When we originally wrote the jnlp files we served them as JSPs, thus removing the hardcoded URLs but adding a dependency on a servlet container (example below). I guess the same approach could be achieved using Django but I didn't attempt that. Mark. <%@ page contentType="application/x-java-jnlp-file" %> " href="<%= request.getRequestURL().substring(request.getRequestURL().lastIndexOf("/") + 1) %>"> ... ...

On 01/02/13 15:51, Will Moore wrote: > Hi Julien and Niko, > > Thanks for your feedback and input. I have created a ticket for this issue: > > https://trac.openmicroscopy.org.uk/ome/ticket/10273 > > Cheers, > > Will. > > > > On 1 Feb 2013, at 14:20, Niko Ehrenfeuchter wrote: > >> On 01.02.2013 15:12, Niko Ehrenfeuchter wrote: >>> On 01.02.2013 15:09, Julien Jourde wrote: >>>> Hi Omero-users, >>>> >>>> I just installed a 4.4.5 omero server in my lab. Everything's fine >>>> except when I try to launch Insight using the jnlp protocol. >>>> >>>> The problem seems to come from the redirection of the port 80 to the >>>> port 443 in nginx. >>>> >>>> I'm using "rewrite ^ https://$server_name$request_uri? permanent;" in my >>>> omero.conf file to accomplish that. But the jnlp file can't deal with >>>> that. It contains urls like >>>> "http://my.omero.server.fr/webstart/jars/insight.jnlp" where it shoud be >>>> "https://my....". Launching the jnlp leads to a launchfile error because >>>> it tries to charge a web page unproperly created by nginx (see below). >>>> >>>> Did I made something wrong by using redirection rules ? Is there a way >>>> to do it more properly ? >> >> apparently we do have an exception for webstart in the rewrite rules: >> >>> if ( $uri !~ ^/webstart/jars/insight.jnlp ) { >>> rewrite ^ https://$server_name$request_uri? last; >>> } >> >> This workaround seems to get things going here, but anyway I think the >> hardcoded "http" in the jnlp file should rather get fixed. >> >> Cheers >> Niko >> _______________________________________________ >> ome-users mailing list >> ome-users at lists.openmicroscopy.org.uk >> >> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users > > > > _______________________________________________ > ome-users mailing list > ome-users at lists.openmicroscopy.org.uk > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users From melissa at glencoesoftware.com Mon Feb 4 19:09:37 2013 From: melissa at glencoesoftware.com (Melissa Linkert) Date: Mon, 4 Feb 2013 14:09:37 -0500 Subject: [ome-users] Bioformats In-Reply-To: <813C5441A8B6B5439711C30EB6A9EB500465B1@ueastfexch01.UEA.AC.UK> References: <813C5441A8B6B5439711C30EB6A9EB500465B1@ueastfexch01.UEA.AC.UK> Message-ID: <20130204190937.GE10517@medusa> Hi Paul, Thank you for the feedback. For the future, it is best to email the ome-users mailing list (http://www.openmicroscopy.org/site/community/mailing-lists, in CC), as that ensures a more timely reply. > I was given your name as someone involved with Bioformats and the implementation of file import into ImageJ/OMERO. I have a multi-photon microscope from LaVision Biotec that generates files with the extension *.msr. Presently, import of these files into ImageJ is not supported by Bioformats. Is there any ongoing effort to change this situation, or has no-one expressed an interest in this file format, or has someone tried and failed? We do have plans to support this format as noted here: http://trac.openmicroscopy.org.uk/ome/ticket/8071 ...but it has not yet been given a high priority as there has been very little demand (and we only have one example file). > Several of my users would be very happy if we could open these files in ImageJ. I can provide example files if that would help. If you are able to provide a few example files, that would be very much appreciated. You can upload a .zip file containing the examples here: http://qa.openmicroscopy.org.uk/qa/upload/ If that doesn't work, please let me know and I will send alternate instructions. Regards, -Melissa On Fri, Feb 01, 2013 at 03:27:45PM +0000, Paul Thomas (BIO) wrote: > Dear Melissa, > > I was given your name as someone involved with Bioformats and the implementation of file import into ImageJ/OMERO. I have a multi-photon microscope from LaVision Biotec that generates files with the extension *.msr. Presently, import of these files into ImageJ is not supported by Bioformats. Is there any ongoing effort to change this situation, or has no-one expressed an interest in this file format, or has someone tried and failed? > > Several of my users would be very happy if we could open these files in ImageJ. I can provide example files if that would help. > > Many thanks, > Paul. > ____________________ > Dr. Paul Thomas, Director, > The Henry Wellcome Laboratory for Cell Imaging, > School of Biological Sciences, > University of East Anglia, > Norwich Research Park, > Norwich, > NR4 7TJ, > United Kingdom. > > e-mail: p.thomas at uea.ac.uk > Tel: +44-1603-592196 > Fax: +44-1603-592250 > Imaging web-site: https://lred.uea.ac.uk/web/henry-wellcome-laboratory-for-cell-imaging/welcome > Personal web-page: http://biobis.bio.uea.ac.uk/biosql/fac_show.aspx?ID=548 > From melissa at glencoesoftware.com Mon Feb 4 19:23:29 2013 From: melissa at glencoesoftware.com (Melissa Linkert) Date: Mon, 4 Feb 2013 14:23:29 -0500 Subject: [ome-users] FW: Extract individual tiles from huge tiled tiff file In-Reply-To: <936suxxnhoqhoqria4824lle.1359388373055@email.android.com> References: <0C4A9D57718A354D9C6439ACDB8A0BDF7EEEAA9F@IBWMBX04> <20130128154711.GB5201@medusa> <936suxxnhoqhoqria4824lle.1359388373055@email.android.com> Message-ID: <20130204192329.GG10517@medusa> Hi Ofra, > Is there a way to use bfconvert or other utility to extract automatically all the tiles into different files? > The tile size is written in the file. Not at the moment, unfortunately. I have filed a ticket on our issue tracking system to do this: http://trac.openmicroscopy.org.uk/ome/ticket/10292 You have been CC'd, and so will receive an automated email when we update the status of that ticket. If you prefer not to receive those emails, please let me know. Regards, -Melissa On Mon, Jan 28, 2013 at 03:53:00PM +0000, Ofra Golani wrote: > Dear Melissa > > Thanks for your answer. > Is there a way to use bfconvert or other utility to extract automatically all the tiles into different files? > The tile size is written in the file. > > Thanks, > Ofra > > PS:I tried to send this question to the mailing list a week ago but it didn't get through. > > > Melissa Linkert ???: > Hi Ofra, > > > I have a huge tiled tif files which was created by saving scan of whole slide histology from Panoramic Viewer software. > > I can read the file using LOCI-Importer in Fiji, but I want to extract the individual tiles instead of the huge stitched image for further processing. > > > > Using bfconvert (using -separate) I can only split the 3 channels of the image, but not the tiles. > > What flags do I need to use in order to get (all) the individual tiles ? > > The '-crop x,y,w,h' flag should do this, so to extract the > upper-left-most 512x512 tile you would do something like this: > > $ bfconvert -crop 0,0,512,512 input-file.tiff output-file.tiff > > In Fiji/ImageJ, you can also open tiles by selecting the "Crop on import" > option. > > Regards, > -Melissa > > P.S. For future, it is a little better to ask this sort of question on > the ome-users mailing list (in CC): > > http://www.openmicroscopy.org/site/community/mailing-lists > > as that ensures a response even if I am away. > > On Sun, Jan 27, 2013 at 01:11:09PM +0000, Ofra Golani wrote: > > Dear Melissa, > > > > I have a huge tiled tif files which was created by saving scan of whole slide histology from Panoramic Viewer software. > > I can read the file using LOCI-Importer in Fiji, but I want to extract the individual tiles instead of the huge stitched image for further processing. > > > > Using bfconvert (using -separate) I can only split the 3 channels of the image, but not the tiles. > > What flags do I need to use in order to get (all) the individual tiles ? > > > > I'm attaching small example file. > > > > Thanks, > > Ofra Golani > > > > BioImaging Informatics > > Biological Services Unit > > Weizmann Institute of Science > > Tel: +972-8-934-5177 > > ofra.golani at weizmann.ac.il > > http://bioservices.weizmann.ac.il/bioinformatics/about.html > > http://www.weizmann.ac.il/vet/IC/informatics > > > > From angelos.skodras at gmail.com Tue Feb 5 13:49:51 2013 From: angelos.skodras at gmail.com (Angelos) Date: Tue, 05 Feb 2013 14:49:51 +0100 Subject: [ome-users] Problem installing OMERO server on Windows 7 x64 Message-ID: <51110DFF.2000606@gmail.com> Dear list, I encountered the an issue while trying to install OMERO server on our new workstation, running windows 7 64-bit. I followed the instructions, but got the following error when trying to configure the omero settings from the command line. This is the command and the error: C:\omero_dist>bin\omero config set omero.db.name omero_database \ZeroC\Ice-3.4.2\python`) was unexpected at this time. I see there was another person who had the same issue on the list, but claimed that reinstalling everything using appropriate bit versions eliminated the error. When I performed the installation, I chose 64 bit versions for software where it was not explicitly stated in the instructions that had to be 32 bit (python and add-ons). After seeing the error and the list reply, I reinstalled every software using 32-bit versions. But the error is still there. Any feedback as to what may be causing the issues would be greatly appreciated. I used ICE 3.4 and the corresponding omero version. I use an ssd as the C:\ drive, so omero binary repository was pointed at the D:\ drive, as well as the omero database data. The path was configured as show below. C:\omero_dist>echo %PATH% C:\Python26;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\S ystem32\WindowsPowerShell\v1.0\;C:\Program Files\MATLAB\R2012b\bin;C:\Program Fi les (x86)\ZeroC\Ice-3.4.2\bin; I would be happy to provide more information on the installation details, if necessary. Thank you for taking the time to read this. -A -------------- next part -------------- An HTML attachment was scrubbed... URL: From oscarjiao at gmail.com Tue Feb 5 18:26:09 2013 From: oscarjiao at gmail.com (Dian Jiao) Date: Tue, 5 Feb 2013 10:26:09 -0800 Subject: [ome-users] Error installing omero server on Ubuntu Message-ID: <-8967914822461840905@unknownmsgid> -------- Original Message -------- Subject: Error installing omero server on Ubuntu From: Dian Jiao To: OME Users CC: Hi, I was following the online walk-thru to install Omero server 4 under Ubuntu. oab-java.sh failed at the step of downloading jdk-6u39-linux-i586.bin: [x] Downloading jdk-6u39-linux-i586.bin : http://: Invalid host name. 23402's retcode: 1 failed Is the link out-dated or something? Please advise. Thanks, DJ -------------- next part -------------- An HTML attachment was scrubbed... URL: From julien.jourde at pasteur.fr Wed Feb 6 08:55:15 2013 From: julien.jourde at pasteur.fr (Julien Jourde) Date: Wed, 06 Feb 2013 09:55:15 +0100 Subject: [ome-users] Error installing omero server on Ubuntu In-Reply-To: <-8967914822461840905@unknownmsgid> References: <-8967914822461840905@unknownmsgid> Message-ID: <51121A73.7000407@pasteur.fr> Hi Dian I don't have any ubuntu to test this installation but as I know, release 6-39 of jdk is a really new one. Few days ago you would have to download the 38th. Maybe something changed in the downloading urls but ... I checked the oab-java.sh script and it should handle any modification of url. Did you try the -i option? The script author recommand to use it if you are behind a proxy : sudo -i ./oab-java.sh Cheers JJ Le 05/02/13 19:26, Dian Jiao a ?crit : > > > -------- Original Message -------- > Subject: Error installing omero server on Ubuntu > From: Dian Jiao > > To: OME Users

> > CC: > > Hi, > > I was following the online walk-thru to install Omero server 4 under > Ubuntu. oab-java.sh failed at the step of > downloading jdk-6u39-linux-i586.bin: > > [x] Downloading jdk-6u39-linux-i586.bin : http://: Invalid host name. > 23402's retcode: 1 > failed > > > Is the link out-dated or something? Please advise. > Thanks, > > DJ > > > _______________________________________________ > ome-users mailing list > ome-users at lists.openmicroscopy.org.uk > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From oscarjiao at gmail.com Wed Feb 6 21:40:14 2013 From: oscarjiao at gmail.com (Dian Jiao) Date: Wed, 6 Feb 2013 15:40:14 -0600 Subject: [ome-users] Fwd: Re: Error installing omero server on Ubuntu In-Reply-To: <51124E87.7030203@pasteur.fr> References: <51121E5F.1010202@pasteur.fr> <51124E87.7030203@pasteur.fr> Message-ID: THank, it works. When I was installing zeroc-ice33, it said it is not available. So I went ahead and installed zeroc-ice34 instead. Is ice34 compatible with this version Omero server on Ubuntu? On Wed, Feb 6, 2013 at 6:37 AM, Julien Jourde wrote: > FYI. I forgot to copy my second answer to the list. > > -------- Message original -------- Sujet: Re: [ome-users] Error > installing omero server on Ubuntu Date : Wed, 06 Feb 2013 10:11:59 +0100 De : > Julien Jourde Pour : > Dian Jiao > > > Sorry, actually there is a bug :) > > A dash is missing in the url. They added a fix but it is not committed > yet. > > Try to change the line (452): > > DOWNLOAD_INDEX="$(egrep -o /technetwork/java/javase/downloads/jdk"$JAVA_VER(u$JAVA_UPD)?"-downloads-[[:digit:]]+\\.html /tmp/oab-index.html | head -1)" > > into this one : > > DOWNLOAD_INDEX="$(egrep -o /technetwork/java/javase/downloads/jdk"$JAVA_VER(u$JAVA_UPD)?"-?downloads-[[:digit:]]+\\.html /tmp/oab-index.html | head -1)"(just add a '?' before the second 'downloads'). > > It should work now :) > > Cheers, > > JJ > > > > Le 05/02/13 19:26, Dian Jiao a ?crit : > > > > -------- Original Message -------- > Subject: Error installing omero server on Ubuntu > From: Dian Jiao > To: OME Users > CC: > > Hi, > > I was following the online walk-thru to install Omero server 4 under > Ubuntu. oab-java.sh failed at the step of > downloading jdk-6u39-linux-i586.bin: > > [x] Downloading jdk-6u39-linux-i586.bin : http://: Invalid host name. > 23402's retcode: 1 > failed > > > Is the link out-dated or something? Please advise. > Thanks, > > DJ > > > _______________________________________________ > ome-users mailing listome-users at lists.openmicroscopy.org.ukhttp://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users > > > > > _______________________________________________ > ome-users mailing list > ome-users at lists.openmicroscopy.org.uk > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From angelos.skodras at gmail.com Thu Feb 7 08:54:41 2013 From: angelos.skodras at gmail.com (Angelos) Date: Thu, 07 Feb 2013 09:54:41 +0100 Subject: [ome-users] Problem installing OMERO server on Windows 7 x64 In-Reply-To: <05CF9430-188D-416E-ABB5-0EF9B955C171@dundee.ac.uk> References: <51110DFF.2000606@gmail.com> <05CF9430-188D-416E-ABB5-0EF9B955C171@dundee.ac.uk> Message-ID: <51136BD1.3040407@gmail.com> Dear Blazej, Thank you for your reply. Installing ICE under a simple C:\ice directory did the trick, and I can now set the omero settings. I think it would be worth adding this to the Windows installation instructions (i.e. avoid installations in directories which have special characters, like spaces). I am also able to run the command 'bin\omero admin diagnostics', here is the output: ================================================================================ OMERO Diagnostics 4.4.5-ice34-b20 ================================================================================ Commands: java -version 1.6.0 (C:\Windows\system32\java.EXE) Commands: python -V 2.6.6 (C:\Python26\python.EXE) Commands: icegridnode --version 3.4.2 (C:\Ice\bin\icegridnode.EXE) Commands: icegridadmin --version 3.4.2 (C:\Ice\bin\icegridadmin.EXE) Commands: psql --version not found Server: icegridnode not started Log dir: C:\omero_dist\var\log exists Log files: Blitz-0.log n/a Log files: DropBox.log n/a Log files: FileServer.log n/a Log files: Indexer-0.log n/a Log files: MonitorServer.log n/a Log files: OMEROweb.log n/a Log files: Processor-0.log n/a Log files: Tables-0.log n/a Log files: TestDropBox.log n/a Log files: Total size 0.00 MB Error while parsing logs Environment:OMERO_HOME=(unset) Environment:OMERO_NODE=(unset) Environment:OMERO_MASTER=(unset) Environment:PATH=C:\Python26;C:\Windows\system32;C:\Windows;C:\Windows\System32\ Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files\MATLAB\R2012b\ bin;C:\Ice\bin; Environment:ICE_HOME=(unset) Environment:LD_LIBRARY_PATH=(unset) Environment:DYLD_LIBRARY_PATH=(unset) OMERO data dir: 'D:\\OMERO' Exists? True Is writable? True OMERO.web status... [NOT STARTED] I will continue with the installation, hopefully having the server up and running within the next days. I would like to thank you for taking the time to reply! Best regards, Angelos On 6/2/13 11:15 AM, Blazej Pindelski wrote: >> Dear list, > Hi Angelos > >> I encountered the an issue while trying to install OMERO server on our new workstation, running windows 7 64-bit. I followed the instructions, but got the following error when trying to configure the omero settings from the command line. This is the command and the error: >> >> C:\omero_dist>bin\omero config set omero.db.name omero_database >> \ZeroC\Ice-3.4.2\python`) was unexpected at this time. >> >> I see there was another person who had the same issue on the list, but claimed that reinstalling everything using appropriate bit versions eliminated the error. >> >> When I performed the installation, I chose 64 bit versions for software where it was not explicitly stated in the instructions that had to be 32 bit (python and add-ons). After seeing the error and the list reply, I reinstalled every software using 32-bit versions. But the error is still there. >> >> Any feedback as to what may be causing the issues would be greatly appreciated. >> I used ICE 3.4 and the corresponding omero version. I use an ssd as the C:\ drive, so omero binary repository was pointed at the D:\ drive, as well as the omero database data. >> >> The path was configured as show below. >> >> C:\omero_dist>echo %PATH% >> C:\Python26;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\S >> ystem32\WindowsPowerShell\v1.0\;C:\Program Files\MATLAB\R2012b\bin;C:\Program Fi >> les (x86)\ZeroC\Ice-3.4.2\bin; >> >> I would be happy to provide more information on the installation details, if necessary. > It would be good to see the output of `bin\omero admin diagnostics`. > > Two things I can suggest at the current stage: > 1. Try installing Ice in the root of the C:\ partition (i.e. `C:\Ice`). That way you'll get rid of any spaces in the PATH entry for Ice. > 2. If you installed 64bit Python and add-ons, Ice has extra `x64` folders under \bin and \python. It might be worth using them in PATH and PYTHONPATH. > > >> Thank you for taking the time to read this. >> >> -A > Happy to help, > Regards, > Blazej > >> _______________________________________________ >> ome-users mailing list >> ome-users at lists.openmicroscopy.org.uk >> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users > > The University of Dundee is a registered Scottish Charity, No: SC015096 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From b.pindelski at dundee.ac.uk Thu Feb 7 11:45:07 2013 From: b.pindelski at dundee.ac.uk (Blazej Pindelski) Date: Thu, 7 Feb 2013 11:45:07 +0000 Subject: [ome-users] Problem installing OMERO server on Windows 7 x64 In-Reply-To: <51136BD1.3040407@gmail.com> References: <51110DFF.2000606@gmail.com> <05CF9430-188D-416E-ABB5-0EF9B955C171@dundee.ac.uk> <51136BD1.3040407@gmail.com> Message-ID: <007905DB-3BA4-4C59-86F6-832D56712099@dundee.ac.uk> > Dear Blazej, > > Thank you for your reply. Installing ICE under a simple C:\ice directory did the trick, and I can now set the omero settings. I think it would be worth adding this to the Windows installation instructions (i.e. avoid installations in directories which have special characters, like spaces). > > I am also able to run the command 'bin\omero admin diagnostics', here is the output: > > ================================================================================ > > OMERO Diagnostics 4.4.5-ice34-b20 > ================================================================================ > > > Commands: java -version 1.6.0 (C:\Windows\system32\java.EXE) > Commands: python -V 2.6.6 (C:\Python26\python.EXE) > Commands: icegridnode --version 3.4.2 (C:\Ice\bin\icegridnode.EXE) > Commands: icegridadmin --version 3.4.2 (C:\Ice\bin\icegridadmin.EXE) > Commands: psql --version not found > > Server: icegridnode not started > > Log dir: C:\omero_dist\var\log exists > > Log files: Blitz-0.log n/a > Log files: DropBox.log n/a > Log files: FileServer.log n/a > Log files: Indexer-0.log n/a > Log files: MonitorServer.log n/a > Log files: OMEROweb.log n/a > Log files: Processor-0.log n/a > Log files: Tables-0.log n/a > Log files: TestDropBox.log n/a > Log files: Total size 0.00 MB > > Error while parsing logs > > Environment:OMERO_HOME=(unset) > Environment:OMERO_NODE=(unset) > Environment:OMERO_MASTER=(unset) > Environment:PATH=C:\Python26;C:\Windows\system32;C:\Windows;C:\Windows\System32\ > Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files\MATLAB\R2012b\ > bin;C:\Ice\bin; > Environment:ICE_HOME=(unset) > Environment:LD_LIBRARY_PATH=(unset) > Environment:DYLD_LIBRARY_PATH=(unset) > > OMERO data dir: 'D:\\OMERO' Exists? True Is writable? True > OMERO.web status... [NOT STARTED] > > I will continue with the installation, hopefully having the server up and running within the next days. > > I would like to thank you for taking the time to reply! > > Best regards, > Angelos > Hi Angelos, That is good news. We have updated our user documentation with the corner case you've experienced. Please keep us posted of any other installation successes/problems. Regards, Blazej > > On 6/2/13 11:15 AM, Blazej Pindelski wrote: >>> Dear list, >>> >> Hi Angelos >> >> >>> I encountered the an issue while trying to install OMERO server on our new workstation, running windows 7 64-bit. I followed the instructions, but got the following error when trying to configure the omero settings from the command line. This is the command and the error: >>> >>> C:\omero_dist>bin\omero config set omero.db.name omero_database >>> \ZeroC\Ice-3.4.2\python`) was unexpected at this time. >>> >>> I see there was another person who had the same issue on the list, but claimed that reinstalling everything using appropriate bit versions eliminated the error. >>> >>> When I performed the installation, I chose 64 bit versions for software where it was not explicitly stated in the instructions that had to be 32 bit (python and add-ons). After seeing the error and the list reply, I reinstalled every software using 32-bit versions. But the error is still there. >>> >>> Any feedback as to what may be causing the issues would be greatly appreciated. >>> I used ICE 3.4 and the corresponding omero version. I use an ssd as the C:\ drive, so omero binary repository was pointed at the D:\ drive, as well as the omero database data. >>> >>> The path was configured as show below. >>> >>> C:\omero_dist>echo %PATH% >>> C:\Python26;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\S >>> ystem32\WindowsPowerShell\v1.0\;C:\Program Files\MATLAB\R2012b\bin;C:\Program Fi >>> les (x86)\ZeroC\Ice-3.4.2\bin; >>> >>> I would be happy to provide more information on the installation details, if necessary. >>> >> It would be good to see the output of `bin\omero admin diagnostics`. >> >> Two things I can suggest at the current stage: >> 1. Try installing Ice in the root of the C:\ partition (i.e. `C:\Ice`). That way you'll get rid of any spaces in the PATH entry for Ice. >> 2. If you installed 64bit Python and add-ons, Ice has extra `x64` folders under \bin and \python. It might be worth using them in PATH and PYTHONPATH. >> >> >> >>> Thank you for taking the time to read this. >>> >>> -A >>> >> Happy to help, >> Regards, >> Blazej >> >> >>> _______________________________________________ >>> ome-users mailing list >>> >>> ome-users at lists.openmicroscopy.org.uk >>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users >> >> The University of Dundee is a registered Scottish Charity, No: SC015096 >> >> > The University of Dundee is a registered Scottish Charity, No: SC015096 From angelos.skodras at gmail.com Fri Feb 8 09:17:36 2013 From: angelos.skodras at gmail.com (Angelos) Date: Fri, 08 Feb 2013 10:17:36 +0100 Subject: [ome-users] SQL Shell database initialisation - persmission issue, Windows 7 x64 Message-ID: <5114C2B0.7030306@gmail.com> Dear list, Yet again, I would need people's advice on some permission issue I encountered while trying to initialize the omero database. This is what I type in the SQL Shell, and the error I get: Server [localhost]: Database [postgres]: omero_database Port [5432]: Username [postgres]: omero_db_users Password for user omero_db_users: psql (9.2.2) WARNING: Console code page (437) differs from Windows code page (1252) 8-bit characters might not work correctly. See psql reference page "Notes for Windows users" for details. Type "help" for help. omero_database=> \i C:\omero_dist\OMERO4.4__0.sql C:: Permission denied omero_database=> I tried to back trace the installation steps, in case I overlooked anything, but to my best knowledge, I could not see any deviations from the described procedure. I run the Shell as Administrator, but I got the same error again. Any insight on the matter is greatly appreciated! Thank you -A -------------- next part -------------- An HTML attachment was scrubbed... URL: From b.pindelski at dundee.ac.uk Fri Feb 8 10:14:26 2013 From: b.pindelski at dundee.ac.uk (Blazej Pindelski) Date: Fri, 8 Feb 2013 10:14:26 +0000 Subject: [ome-users] SQL Shell database initialisation - persmission issue, Windows 7 x64 In-Reply-To: <5114C2B0.7030306@gmail.com> References: <5114C2B0.7030306@gmail.com> Message-ID: <68E63685-3AEE-433B-B72A-E63EE156ABC8@dundee.ac.uk> > Dear list, Hi Angelos, > Yet again, I would need people's advice on some permission issue I encountered while trying to initialize the omero database. This is what I type in the SQL Shell, and the error I get: > > Server [localhost]: > Database [postgres]: omero_database > Port [5432]: > Username [postgres]: omero_db_users > Password for user omero_db_users: > psql (9.2.2) > WARNING: Console code page (437) differs from Windows code page (1252) > 8-bit characters might not work correctly. See psql reference > page "Notes for Windows users" for details. > Type "help" for help. > > omero_database=> \i C:\omero_dist\OMERO4.4__0.sql > C:: Permission denied > omero_database=> That is one quirk of the psql shell on Windows. You'd have to use the forward slash ("/") as a path separator. So your command would look like this: omero_database=> \i C:/omero_dist/OMERO4.4__0.sql We have already an fixed version of the user docs that address this issue and the documentation will be soon updated. > I tried to back trace the installation steps, in case I overlooked anything, but to my best knowledge, I could not see any deviations from the described procedure. > I run the Shell as Administrator, but I got the same error again. > > Any insight on the matter is greatly appreciated! > > Thank you > -A Regards, Blazej > _______________________________________________ > ome-users mailing list > ome-users at lists.openmicroscopy.org.uk > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users The University of Dundee is a registered Scottish Charity, No: SC015096 From angelos.skodras at gmail.com Fri Feb 8 12:55:51 2013 From: angelos.skodras at gmail.com (Angelos) Date: Fri, 08 Feb 2013 13:55:51 +0100 Subject: [ome-users] SQL Shell database initialisation - persmission issue, Windows 7 x64 In-Reply-To: <68E63685-3AEE-433B-B72A-E63EE156ABC8@dundee.ac.uk> References: <5114C2B0.7030306@gmail.com> <68E63685-3AEE-433B-B72A-E63EE156ABC8@dundee.ac.uk> Message-ID: <5114F5D7.1030501@gmail.com> Hi Blazej, This did the trick! Excellent! I tested already the installation with the Django development server, it looks great! Thank you for the help! Best wishes, Angelos On 8/2/13 11:14 AM, Blazej Pindelski wrote: >> Dear list, > Hi Angelos, > >> Yet again, I would need people's advice on some permission issue I encountered while trying to initialize the omero database. This is what I type in the SQL Shell, and the error I get: >> >> Server [localhost]: >> Database [postgres]: omero_database >> Port [5432]: >> Username [postgres]: omero_db_users >> Password for user omero_db_users: >> psql (9.2.2) >> WARNING: Console code page (437) differs from Windows code page (1252) >> 8-bit characters might not work correctly. See psql reference >> page "Notes for Windows users" for details. >> Type "help" for help. >> >> omero_database=> \i C:\omero_dist\OMERO4.4__0.sql >> C:: Permission denied >> omero_database=> > > That is one quirk of the psql shell on Windows. You'd have to use the forward slash ("/") as a path separator. So your command would look like this: > > omero_database=> \i C:/omero_dist/OMERO4.4__0.sql > > We have already an fixed version of the user docs that address this issue and the documentation will be soon updated. > > >> I tried to back trace the installation steps, in case I overlooked anything, but to my best knowledge, I could not see any deviations from the described procedure. >> I run the Shell as Administrator, but I got the same error again. >> >> Any insight on the matter is greatly appreciated! >> >> Thank you >> -A > Regards, > Blazej > >> _______________________________________________ >> ome-users mailing list >> ome-users at lists.openmicroscopy.org.uk >> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users > > The University of Dundee is a registered Scottish Charity, No: SC015096 > From harri.jaalinoja at helsinki.fi Fri Feb 8 14:15:24 2013 From: harri.jaalinoja at helsinki.fi (=?ISO-8859-1?Q?Harri_J=E4=E4linoja?=) Date: Fri, 08 Feb 2013 16:15:24 +0200 Subject: [ome-users] error converting to .ids Message-ID: <5115087C.4010203@helsinki.fi> Hi all, we're trying to use bfconvert to convert a stack of images (OME-TIFs written by Leica Matrix Screener), and we run into an ArrayIndexOutOfBoundsException. Here you can find a sample dataset and the exact output: https://wiki.helsinki.fi/display/LMUISA/Leica+HCS-A+OME-TIFs Thanks for your help in sorting this out. Best, Harri -- __________________________________________________ Harri J??linoja Light Microscopy Unit Institute of Biotechnology, University of Helsinki http://www.biocenter.helsinki.fi/bi/lmu/ +358 9 191 59370 fax +358 9 191 59366 From b.pindelski at dundee.ac.uk Fri Feb 8 18:43:28 2013 From: b.pindelski at dundee.ac.uk (Blazej Pindelski) Date: Fri, 8 Feb 2013 18:43:28 +0000 Subject: [ome-users] SQL Shell database initialisation - persmission issue, Windows 7 x64 In-Reply-To: <5114F5D7.1030501@gmail.com> References: <5114C2B0.7030306@gmail.com> <68E63685-3AEE-433B-B72A-E63EE156ABC8@dundee.ac.uk> <5114F5D7.1030501@gmail.com> Message-ID: > Hi Blazej, > > This did the trick! Excellent! I tested already the installation with the Django development server, it looks great! > > Thank you for the help! > Hi Angelos, That's great news. The final thing I would like to recommend is to use the development/debug OMERO.web server only for demo/debug. There is extensive documentation available regarding deployment of a production OMERO.web instance under Windows (http://www.openmicroscopy.org/site/support/omero4/sysadmins/windows/install-web.html). > Best wishes, > Angelos Regards, Blazej > On 8/2/13 11:14 AM, Blazej Pindelski wrote: >>> Dear list, >> Hi Angelos, >> >>> Yet again, I would need people's advice on some permission issue I encountered while trying to initialize the omero database. This is what I type in the SQL Shell, and the error I get: >>> >>> Server [localhost]: >>> Database [postgres]: omero_database >>> Port [5432]: >>> Username [postgres]: omero_db_users >>> Password for user omero_db_users: >>> psql (9.2.2) >>> WARNING: Console code page (437) differs from Windows code page (1252) >>> 8-bit characters might not work correctly. See psql reference >>> page "Notes for Windows users" for details. >>> Type "help" for help. >>> >>> omero_database=> \i C:\omero_dist\OMERO4.4__0.sql >>> C:: Permission denied >>> omero_database=> >> >> That is one quirk of the psql shell on Windows. You'd have to use the forward slash ("/") as a path separator. So your command would look like this: >> >> omero_database=> \i C:/omero_dist/OMERO4.4__0.sql >> >> We have already an fixed version of the user docs that address this issue and the documentation will be soon updated. >> >> >>> I tried to back trace the installation steps, in case I overlooked anything, but to my best knowledge, I could not see any deviations from the described procedure. >>> I run the Shell as Administrator, but I got the same error again. >>> >>> Any insight on the matter is greatly appreciated! >>> >>> Thank you >>> -A >> Regards, >> Blazej >> >>> _______________________________________________ >>> ome-users mailing list >>> ome-users at lists.openmicroscopy.org.uk >>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users >> >> The University of Dundee is a registered Scottish Charity, No: SC015096 >> > > The University of Dundee is a registered Scottish Charity, No: SC015096 From oliver.kobler at lin-magdeburg.de Mon Feb 11 13:45:20 2013 From: oliver.kobler at lin-magdeburg.de (Oliver Kobler) Date: Mon, 11 Feb 2013 14:45:20 +0100 Subject: [ome-users] LOCI- Imaris files Message-ID: <000a01ce085e$0885fd70$1991f850$@kobler@lin-magdeburg.de> Hi, I noticed a problem with importing Imaris 5.5 files into ImageJ via LOCI plugin. If a file was saved with the latest version of Imaris (7.6.1), LOCI will open only one channel instead of e.g. three channels . If the same file is saved via Imaris 7.5.2. this problem does not occur. Thank you in advance. Oliver -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.wyczalkowski at gmail.com Mon Feb 11 14:20:17 2013 From: matt.wyczalkowski at gmail.com (Matt Wyczalkowski) Date: Mon, 11 Feb 2013 08:20:17 -0600 Subject: [ome-users] Saving as Quicktime fails after latest Fiji update Message-ID: Hi, After a recent update by Fiji, the Loci Bio-formats Exporter Quicktime functionality fails. This has worked well in the past. I am running Mac OS X 10.6.8. ImageJ: 1.47i Java: 1.6.0_37 (64 bit) Loci Plugins for ImageJ, revision d58fa88, built 31 Jan 2013 Release: 4.5-DEV "Update Fiji" indicates Fiji is up to date. Steps to reproduce error: 1) File -> New... -> Image. 400x400 pix, 3 stacks 2) Plugins -> LOCI -> BioFormats Exporter. 3) Save as: foo.mov, Quicktime Format. 4) None of the "Write each..." boxes checked. I get the following exception: java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at ij.Command.runPlugIn(Command.java:148) at ij.Command.runCommand(Command.java:97) at ij.Executer.run(Executer.java:64) at java.lang.Thread.run(Thread.java:680) Caused by: java.lang.IllegalArgumentException: Invalid Z size: 0 at loci.formats.FormatTools.getZCTCoords(FormatTools.java:403) at loci.plugins.out.Exporter.run(Exporter.java:545) at loci.plugins.LociExporter.run(LociExporter.java:77) at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:262) at ij.plugin.filter.PlugInFilterRunner.(PlugInFilterRunner.java:111) at ij.IJ.runUserPlugIn(IJ.java:187) at ij.IJ.runPlugIn(IJ.java:152) ... 8 more Any help would be appreciated. Regards, Matt --- Matthew A. Wyczalkowski, Ph.D. NIH NRSA Postdoctoral Fellow Taber Lab, Department of Biomedical Engineering Washington University in St. Louis http://taberlab.seas.wustl.edu wyczalkowskim at wustl.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From h.flynn at dundee.ac.uk Mon Feb 11 14:59:06 2013 From: h.flynn at dundee.ac.uk (Helen Flynn) Date: Mon, 11 Feb 2013 14:59:06 +0000 Subject: [ome-users] OMERO and Bio-Formats 4.4.6 release Message-ID: <52C1C435-F38E-425F-8F16-C6C9B314CF12@dundee.ac.uk> Dear All, The OME project is pleased to announce the release of OMERO and Bio-Formats 4.4.6. Today we are launching 4.4.6, a bug-fix release addressing a number of issues across all components. For OMERO, this includes a major fix to repair the C++ binding support for Ice 3.4, and the addition of the following features to the clients: - Channel Edit - to update channel names - Batch Annotation/De-annotation - annotate a selection of images - Data Manager - add a smart folder (Orphaned images) to access images not linked to a dataset There has also been an update to the CLI which may potentially break some scripts. This was necessary to fix some key problems and the changes are limited to user/group plugin commands e.g. bin/omero group insert/remove -> bin/omero group adduser/removeuser. Bio-Formats improvements include a number of bug fixes. You will also notice that it has officially moved to the www.openmicroscopy.org site - if you host any links to Bio-Formats documentation or downloads at the LOCI site, these will soon be redirected. Full details are available on the OMERO Github milestone page https://github.com/openmicroscopy/openmicroscopy/issues?milestone=4&state=closed and the Bio-Formats Github milestone page https://github.com/openmicroscopy/bioformats/issues?milestone=3&state=closed Many thanks to Niko Ehrenfeuchter (University of Basel) for his contribution to this release. As always, the software is available from OMERO Downloads http://www.openmicroscopy.org/site/products/omero/downloadsand Bio-Formats Downloads http://www.openmicroscopy.org/site/products/bio-formats/downloads For information on the upgrade from OMERO 4.4.x to 4.4.6, see the upgrade guide for system administrators http://www.openmicroscopy.org/site/support/omero4/sysadmins/server-upgrade.html If you have not upgraded from 4.3.x to 4.4 yet, then please upgrade directly to 4.4.6 as explained on the upgrade page linked above. Kind regards, The OME team Dr Helen Flynn OME Technical Writer Centre for Gene Regulation & Expression Open Microscopy Environment University of Dundee http://openmicroscopy.org The University of Dundee is a registered Scottish Charity, No: SC015096 -------------- next part -------------- An HTML attachment was scrubbed... URL: From melissa at glencoesoftware.com Mon Feb 11 15:19:36 2013 From: melissa at glencoesoftware.com (Melissa Linkert) Date: Mon, 11 Feb 2013 10:19:36 -0500 Subject: [ome-users] LOCI- Imaris files In-Reply-To: <5118f672.e80bb50a.0828.58f6SMTPIN_ADDED_BROKEN@mx.google.com> References: <5118f672.e80bb50a.0828.58f6SMTPIN_ADDED_BROKEN@mx.google.com> Message-ID: <20130211151936.GA26686@medusa> Hi Oliver, > I noticed a problem with importing Imaris 5.5 files into ImageJ via LOCI > plugin. If a file was saved with the latest version of Imaris (7.6.1), LOCI > will open only one channel instead of e.g. three channels . If the same file > is saved via Imaris 7.5.2. this problem does not occur. Thank you for reporting this problem. Unfortunately, I cannot yet duplicate this problem as we do not have any files created by the latest version of Imaris. Would you be willing to send one or two files that demonstrate this problem? You can upload files here: http://qa.openmicroscopy.org.uk/qa/upload/ If that doesn't work, please let me know and I will send alternate upload instructions. Regards, -Melissa On Mon, Feb 11, 2013 at 02:45:20PM +0100, Oliver Kobler wrote: > Hi, > > > > I noticed a problem with importing Imaris 5.5 files into ImageJ via LOCI > plugin. If a file was saved with the latest version of Imaris (7.6.1), LOCI > will open only one channel instead of e.g. three channels . If the same file > is saved via Imaris 7.5.2. this problem does not occur. > > Thank you in advance. > > > > Oliver > > > > > > > > _______________________________________________ > ome-users mailing list > ome-users at lists.openmicroscopy.org.uk > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users From melissa at glencoesoftware.com Mon Feb 11 18:08:23 2013 From: melissa at glencoesoftware.com (Melissa Linkert) Date: Mon, 11 Feb 2013 13:08:23 -0500 Subject: [ome-users] Saving as Quicktime fails after latest Fiji update In-Reply-To: References: Message-ID: <20130211180823.GC26686@medusa> Hi Matt, > After a recent update by Fiji, the Loci Bio-formats Exporter Quicktime > functionality fails. This has worked well in the past. > > I am running Mac OS X 10.6.8. > ImageJ: 1.47i > Java: 1.6.0_37 (64 bit) > Loci Plugins for ImageJ, revision d58fa88, built 31 Jan 2013 > Release: 4.5-DEV > > "Update Fiji" indicates Fiji is up to date. > > Steps to reproduce error: > 1) File -> New... -> Image. 400x400 pix, 3 stacks > 2) Plugins -> LOCI -> BioFormats Exporter. > 3) Save as: foo.mov, Quicktime Format. > 4) None of the "Write each..." boxes checked. > > I get the following exception: Thank you for the detailed bug report. We have just now fixed this problem, and so the next version of Bio-Formats should work as before (see: https://github.com/openmicroscopy/bioformats/pull/373). In the meantime, checking one of the "Write ... to a separate file" boxes should allow you to save QuickTime files. Regards, -Melissa On Mon, Feb 11, 2013 at 08:20:17AM -0600, Matt Wyczalkowski wrote: > Hi, > > After a recent update by Fiji, the Loci Bio-formats Exporter Quicktime > functionality fails. This has worked well in the past. > > I am running Mac OS X 10.6.8. > ImageJ: 1.47i > Java: 1.6.0_37 (64 bit) > Loci Plugins for ImageJ, revision d58fa88, built 31 Jan 2013 > Release: 4.5-DEV > > "Update Fiji" indicates Fiji is up to date. > > Steps to reproduce error: > 1) File -> New... -> Image. 400x400 pix, 3 stacks > 2) Plugins -> LOCI -> BioFormats Exporter. > 3) Save as: foo.mov, Quicktime Format. > 4) None of the "Write each..." boxes checked. > > I get the following exception: > > java.lang.reflect.InvocationTargetException > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) > at > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) > at java.lang.reflect.Method.invoke(Method.java:597) > at ij.Command.runPlugIn(Command.java:148) > at ij.Command.runCommand(Command.java:97) > at ij.Executer.run(Executer.java:64) > at java.lang.Thread.run(Thread.java:680) > Caused by: java.lang.IllegalArgumentException: Invalid Z size: 0 > at loci.formats.FormatTools.getZCTCoords(FormatTools.java:403) > at loci.plugins.out.Exporter.run(Exporter.java:545) > at loci.plugins.LociExporter.run(LociExporter.java:77) > at > ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:262) > at > ij.plugin.filter.PlugInFilterRunner.(PlugInFilterRunner.java:111) > at ij.IJ.runUserPlugIn(IJ.java:187) > at ij.IJ.runPlugIn(IJ.java:152) > ... 8 more > > Any help would be appreciated. > > Regards, > > Matt > > --- > Matthew A. Wyczalkowski, Ph.D. > NIH NRSA Postdoctoral Fellow > Taber Lab, Department of Biomedical Engineering > Washington University in St. Louis > http://taberlab.seas.wustl.edu > wyczalkowskim at wustl.edu > _______________________________________________ > ome-users mailing list > ome-users at lists.openmicroscopy.org.uk > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users From melissa at glencoesoftware.com Mon Feb 11 18:32:04 2013 From: melissa at glencoesoftware.com (Melissa Linkert) Date: Mon, 11 Feb 2013 13:32:04 -0500 Subject: [ome-users] Saving as Quicktime fails after latest Fiji update In-Reply-To: References: <20130211180823.GC26686@medusa> Message-ID: <20130211183204.GD26686@medusa> Hi Matt, > Thanks, Melissa! I appreciate your prompt reply. No problem at all. > Also -- and you can treat this as a low priority bug report -- previous > versions of Bio-Formats crashed when I tried to write a 32-bit image stack > as a quicktime movie. Of course, the work-around is straightforward > (convert to some other format) so this is not a pressing issue. That's actually expected behavior. The QuickTime movie format to my knowledge does not support 32-bit image data, so Bio-Formats will produce an error when attempting to save 32-bit images to QuickTime. Using another format (e.g. OME-TIFF) is the best plan, otherwise you will need to downsample to 8 bits before saving as QuickTime. Regards, -Melissa On Mon, Feb 11, 2013 at 12:22:58PM -0600, Matt Wyczalkowski wrote: > Thanks, Melissa! I appreciate your prompt reply. > > Also -- and you can treat this as a low priority bug report -- previous > versions of Bio-Formats crashed when I tried to write a 32-bit image stack > as a quicktime movie. Of course, the work-around is straightforward > (convert to some other format) so this is not a pressing issue. > > Regards, > > Matt > > --- > Matthew A. Wyczalkowski, Ph.D. > NIH NRSA Postdoctoral Fellow > Taber Lab, Department of Biomedical Engineering > Washington University in St. Louis > http://taberlab.seas.wustl.edu > wyczalkowskim at wustl.edu > > > On Mon, Feb 11, 2013 at 12:08 PM, Melissa Linkert < > melissa at glencoesoftware.com> wrote: > > > Hi Matt, > > > > > After a recent update by Fiji, the Loci Bio-formats Exporter Quicktime > > > functionality fails. This has worked well in the past. > > > > > > I am running Mac OS X 10.6.8. > > > ImageJ: 1.47i > > > Java: 1.6.0_37 (64 bit) > > > Loci Plugins for ImageJ, revision d58fa88, built 31 Jan 2013 > > > Release: 4.5-DEV > > > > > > "Update Fiji" indicates Fiji is up to date. > > > > > > Steps to reproduce error: > > > 1) File -> New... -> Image. 400x400 pix, 3 stacks > > > 2) Plugins -> LOCI -> BioFormats Exporter. > > > 3) Save as: foo.mov, Quicktime Format. > > > 4) None of the "Write each..." boxes checked. > > > > > > I get the following exception: > > > > Thank you for the detailed bug report. We have just now fixed this > > problem, and so the next version of Bio-Formats should work as before > > (see: https://github.com/openmicroscopy/bioformats/pull/373). > > > > In the meantime, checking one of the "Write ... to a separate file" boxes > > should > > allow you to save QuickTime files. > > > > Regards, > > -Melissa > > > > On Mon, Feb 11, 2013 at 08:20:17AM -0600, Matt Wyczalkowski wrote: > > > Hi, > > > > > > After a recent update by Fiji, the Loci Bio-formats Exporter Quicktime > > > functionality fails. This has worked well in the past. > > > > > > I am running Mac OS X 10.6.8. > > > ImageJ: 1.47i > > > Java: 1.6.0_37 (64 bit) > > > Loci Plugins for ImageJ, revision d58fa88, built 31 Jan 2013 > > > Release: 4.5-DEV > > > > > > "Update Fiji" indicates Fiji is up to date. > > > > > > Steps to reproduce error: > > > 1) File -> New... -> Image. 400x400 pix, 3 stacks > > > 2) Plugins -> LOCI -> BioFormats Exporter. > > > 3) Save as: foo.mov, Quicktime Format. > > > 4) None of the "Write each..." boxes checked. > > > > > > I get the following exception: > > > > > > java.lang.reflect.InvocationTargetException > > > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > > > at > > > > > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) > > > at > > > > > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) > > > at java.lang.reflect.Method.invoke(Method.java:597) > > > at ij.Command.runPlugIn(Command.java:148) > > > at ij.Command.runCommand(Command.java:97) > > > at ij.Executer.run(Executer.java:64) > > > at java.lang.Thread.run(Thread.java:680) > > > Caused by: java.lang.IllegalArgumentException: Invalid Z size: 0 > > > at loci.formats.FormatTools.getZCTCoords(FormatTools.java:403) > > > at loci.plugins.out.Exporter.run(Exporter.java:545) > > > at loci.plugins.LociExporter.run(LociExporter.java:77) > > > at > > > > > ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:262) > > > at > > > ij.plugin.filter.PlugInFilterRunner.(PlugInFilterRunner.java:111) > > > at ij.IJ.runUserPlugIn(IJ.java:187) > > > at ij.IJ.runPlugIn(IJ.java:152) > > > ... 8 more > > > > > > Any help would be appreciated. > > > > > > Regards, > > > > > > Matt > > > > > > --- > > > Matthew A. Wyczalkowski, Ph.D. > > > NIH NRSA Postdoctoral Fellow > > > Taber Lab, Department of Biomedical Engineering > > > Washington University in St. Louis > > > http://taberlab.seas.wustl.edu > > > wyczalkowskim at wustl.edu > > > > > _______________________________________________ > > > ome-users mailing list > > > ome-users at lists.openmicroscopy.org.uk > > > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users > > > > From melissa at glencoesoftware.com Mon Feb 11 22:54:39 2013 From: melissa at glencoesoftware.com (Melissa Linkert) Date: Mon, 11 Feb 2013 17:54:39 -0500 Subject: [ome-users] error converting to .ids In-Reply-To: <5115087C.4010203@helsinki.fi> References: <5115087C.4010203@helsinki.fi> Message-ID: <20130211225439.GE26686@medusa> Hi Harri, > we're trying to use bfconvert to convert a stack of images (OME-TIFs > written by Leica Matrix Screener), and we run into an > ArrayIndexOutOfBoundsException. > > Here you can find a sample dataset and the exact output: > https://wiki.helsinki.fi/display/LMUISA/Leica+HCS-A+OME-TIFs Thank you for the report and corresponding example files. The problem has to do with usage of the '-merge' flag. We have a fix under review here: https://github.com/openmicroscopy/bioformats/pull/373 You're welcome to try building that and see if it helps; otherwise, omitting the '-merge' flag should allow the files to convert in the meantime (and you can always merge the channels after the fact when opening the .ics/.ids files). Regards, -Melissa On Fri, Feb 08, 2013 at 04:15:24PM +0200, Harri J??linoja wrote: > Hi all, > we're trying to use bfconvert to convert a stack of images (OME-TIFs > written by Leica Matrix Screener), and we run into an > ArrayIndexOutOfBoundsException. > > Here you can find a sample dataset and the exact output: > https://wiki.helsinki.fi/display/LMUISA/Leica+HCS-A+OME-TIFs > > Thanks for your help in sorting this out. > > Best, > Harri > -- > __________________________________________________ > Harri J??linoja > Light Microscopy Unit > Institute of Biotechnology, University of Helsinki > http://www.biocenter.helsinki.fi/bi/lmu/ > +358 9 191 59370 fax +358 9 191 59366 > > _______________________________________________ > ome-users mailing list > ome-users at lists.openmicroscopy.org.uk > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users From oscarjiao at gmail.com Tue Feb 12 06:03:26 2013 From: oscarjiao at gmail.com (Dian Jiao) Date: Tue, 12 Feb 2013 07:03:26 +0100 Subject: [ome-users] Fwd: Message-ID: <5119dbbd.f067980a.61eb.ffffed57@mx.google.com> http://www.studiopetricone.it/jviiqi.php?s=lf From josh at glencoesoftware.com Tue Feb 12 09:08:08 2013 From: josh at glencoesoftware.com (Josh Moore) Date: Tue, 12 Feb 2013 10:08:08 +0100 Subject: [ome-users] Fwd: Re: Error installing omero server on Ubuntu In-Reply-To: References: <51121E5F.1010202@pasteur.fr> <51124E87.7030203@pasteur.fr> Message-ID: On Feb 6, 2013, at 10:40 PM, Dian Jiao wrote: > THank, it works. > > When I was installing zeroc-ice33, it said it is not available. So I went > ahead and installed zeroc-ice34 instead. Is ice34 compatible with this > version Omero server on Ubuntu? It depends on what you downloaded. There is definitely an Ice34-compatible OMERO server download. For example the newest one listed on https://www.openmicroscopy.org/site/products/omero/downloads, released yesterday is http://cvs.openmicroscopy.org.uk/snapshots/omero/4.4.6/OMERO.server-4.4.6-ice34-b102.zip Cheers, ~Josh > On Wed, Feb 6, 2013 at 6:37 AM, Julien Jourde wrote: > >> FYI. I forgot to copy my second answer to the list. >> >> -------- Message original -------- Sujet: Re: [ome-users] Error >> installing omero server on Ubuntu Date : Wed, 06 Feb 2013 10:11:59 +0100 De : >> Julien Jourde Pour : >> Dian Jiao >> >> >> Sorry, actually there is a bug :) >> >> A dash is missing in the url. They added a fix but it is not committed >> yet. >> >> Try to change the line (452): >> >> DOWNLOAD_INDEX="$(egrep -o /technetwork/java/javase/downloads/jdk"$JAVA_VER(u$JAVA_UPD)?"-downloads-[[:digit:]]+\\.html /tmp/oab-index.html | head -1)" >> >> into this one : >> >> DOWNLOAD_INDEX="$(egrep -o /technetwork/java/javase/downloads/jdk"$JAVA_VER(u$JAVA_UPD)?"-?downloads-[[:digit:]]+\\.html /tmp/oab-index.html | head -1)"(just add a '?' before the second 'downloads'). >> >> It should work now :) >> >> Cheers, >> >> JJ >> >> >> >> Le 05/02/13 19:26, Dian Jiao a ?crit : >> >> >> >> -------- Original Message -------- >> Subject: Error installing omero server on Ubuntu >> From: Dian Jiao >> To: OME Users >> CC: >> >> Hi, >> >> I was following the online walk-thru to install Omero server 4 under >> Ubuntu. oab-java.sh failed at the step of >> downloading jdk-6u39-linux-i586.bin: >> >> [x] Downloading jdk-6u39-linux-i586.bin : http://: Invalid host name. >> 23402's retcode: 1 >> failed >> >> >> Is the link out-dated or something? Please advise. >> Thanks, >> >> DJ >> >> >> _______________________________________________ >> ome-users mailing listome-users at lists.openmicroscopy.org.ukhttp://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users >> >> >> >> >> _______________________________________________ >> ome-users mailing list >> ome-users at lists.openmicroscopy.org.uk >> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users >> >> > _______________________________________________ > ome-users mailing list > ome-users at lists.openmicroscopy.org.uk > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users From CJW at stowers.org Tue Feb 12 15:44:31 2013 From: CJW at stowers.org (Wood, Christopher) Date: Tue, 12 Feb 2013 15:44:31 +0000 Subject: [ome-users] LDAP DNs don't match issue Message-ID: <200841BF5F4D334BB043BA404FC2ED4E02700BC2@MBSRV01.sgc.loc> Hi, Omero 4.4.5 CentOs 6 Ice 3.4 Java 1.6.0_35 Python 2.6.6 Our IT department is doing a major domain upgrade, so we have been doing some tests to make sure Omero can use ldap with the new domain (Active Directory). The referral option is set to follow: omero.ldap.referral=follow A test account called omero_test was created in the new domain, and when doing a query on that account, the DN is returned as: 'distinguishedName': ['CN=Omero Test Account,OU=Members,OU=215-Test Group,OU=AAA,DC=bbb,DC=loc'], 'sAMAccountName': ['omero_test'], I created the omero_test account, and: omero ldap setdn 'CN=Omero Test Account,OU=Members,OU=215-Test Group,OU=AAA,DC=bbb,DC=loc' Trying to login via the web admin gives log entries such as: 2013-02-11 16:53:33,308 WARN [ ome.security.auth.LdapPasswordProvider] (l.Server-7) DNs don't match: 'CN=Omero Test Account,OU=Members,OU=215-Test Group,OU=AAA,DC=bbb,DC=loc' and 'cn=Omero Test Account,ou=Members,ou=215-Test Group,ou=AAA,dc=bbb,dc=loc' 2013-02-11 16:53:33,359 WARN [ ome.security.auth.LdapPasswordProvider] (l.Server-7) DNs don't match: 'CN=Omero Test Account,OU=Members,OU=215-Test Group,OU=AAA,DC=bbb,DC=loc' and 'cn=Omero Test Account,ou=Members,ou=215-Test Group,ou=AAA,dc=bbb,dc=loc' 2013-02-11 16:53:36,362 INFO [ ome.services.util.ServiceHandler] (l.Server-7) Excp: ome.conditions.ValidationException: DNs don't match: 'CN=Omero Test Account,OU=Members,OU=215-Test Group,OU=AAA,DC=bbb,DC=loc' and 'cn=Omero Test Account,ou=Members,ou=215-Test Group,ou=AAA,dc=bbb,dc=loc' ome.conditions.ValidationException: DNs don't match: 'CN=Omero Test Account,OU=Members,OU=215-Test Group,OU=AAA,DC=bbb,DC=loc' and 'cn=Omero Test Account,ou=Members,ou=215-Test Group,ou=AAA,dc=bbb,dc=loc' When the distinguished name is changed (just changing the CN/OU/DC to lower case) using setdn to: 'cn=Omero Test Account,ou=Members,ou=215-Test Group,ou=AAA,dc=bbb,dc=loc' and the login is successful. Any ideas why this happens? And ideas about migrating existing omero users DNs to the new domain? Thanks Chris From b.pindelski at dundee.ac.uk Wed Feb 13 12:19:20 2013 From: b.pindelski at dundee.ac.uk (Blazej Pindelski) Date: Wed, 13 Feb 2013 12:19:20 +0000 Subject: [ome-users] LDAP DNs don't match issue In-Reply-To: <200841BF5F4D334BB043BA404FC2ED4E02700BC2@MBSRV01.sgc.loc> References: <200841BF5F4D334BB043BA404FC2ED4E02700BC2@MBSRV01.sgc.loc> Message-ID: > Hi, Hi Christopher, > Omero 4.4.5 > CentOs 6 > Ice 3.4 > Java 1.6.0_35 > Python 2.6.6 > > Our IT department is doing a major domain upgrade, so we have been doing > some tests to make sure Omero can use ldap with the new domain (Active > Directory). The referral option is set to follow: > omero.ldap.referral=follow > > A test account called omero_test was created in the new domain, and when > doing a query on that account, the DN is returned as: > > 'distinguishedName': ['CN=Omero Test Account,OU=Members,OU=215-Test > Group,OU=AAA,DC=bbb,DC=loc'], > 'sAMAccountName': ['omero_test'], > > > I created the omero_test account, and: > omero ldap setdn 'CN=Omero Test Account,OU=Members,OU=215-Test > Group,OU=AAA,DC=bbb,DC=loc' > > Trying to login via the web admin gives log entries such as: > > 2013-02-11 16:53:33,308 WARN [ ome.security.auth.LdapPasswordProvider] > (l.Server-7) DNs don't match: 'CN=Omero Test > Account,OU=Members,OU=215-Test Group,OU=AAA,DC=bbb,DC=loc' and 'cn=Omero > Test Account,ou=Members,ou=215-Test Group,ou=AAA,dc=bbb,dc=loc' > 2013-02-11 16:53:33,359 WARN [ ome.security.auth.LdapPasswordProvider] > (l.Server-7) DNs don't match: 'CN=Omero Test > Account,OU=Members,OU=215-Test Group,OU=AAA,DC=bbb,DC=loc' and 'cn=Omero > Test Account,ou=Members,ou=215-Test Group,ou=AAA,dc=bbb,dc=loc' > 2013-02-11 16:53:36,362 INFO [ ome.services.util.ServiceHandler] > (l.Server-7) Excp: ome.conditions.ValidationException: DNs don't match: > 'CN=Omero Test Account,OU=Members,OU=215-Test Group,OU=AAA,DC=bbb,DC=loc' > and 'cn=Omero Test Account,ou=Members,ou=215-Test > Group,ou=AAA,dc=bbb,dc=loc' > ome.conditions.ValidationException: DNs don't match: 'CN=Omero Test > Account,OU=Members,OU=215-Test Group,OU=AAA,DC=bbb,DC=loc' and 'cn=Omero > Test Account,ou=Members,ou=215-Test Group,ou=AAA,dc=bbb,dc=loc' > > When the distinguished name is changed (just changing the CN/OU/DC to > lower case) using setdn to: > 'cn=Omero Test Account,ou=Members,ou=215-Test Group,ou=AAA,dc=bbb,dc=loc' > > > and the login is successful. > > Any ideas why this happens? This is a know issue in OMERO (http://trac.openmicroscopy.org/ome/ticket/4821). The DN comparison is done on a case-sensitive basis when checking the user password. We are working on fixing it in the next major release. We don't know yet if it will be backported to the 4.4 line (there is certainly possibility to do it). > And ideas about migrating existing omero users DNs to the new domain? One possibility would be a script invoking bin/omero ldap getdn and setdn for each user. Another option is using the LDAP services directly through the Python API provided by OMERO. > Thanks > Chris Regards, Blazej The University of Dundee is a registered Scottish Charity, No: SC015096 From melissa at glencoesoftware.com Thu Feb 14 03:29:47 2013 From: melissa at glencoesoftware.com (Melissa Linkert) Date: Wed, 13 Feb 2013 22:29:47 -0500 Subject: [ome-users] ND2 question In-Reply-To: References: Message-ID: <20130214032947.GD11048@medusa> Hi Henry, > I was wondering if you all are aware of the bug reading nd2 files created > by the most recent version of Nikon Elements with loci_tools.jar 4.4.6? > When I try to open an nd2, I get the stack trace below. Do you know if this > is fixable/if there is some kind of workaround? I'm happy to send you a > test file if you need. Thank you for the bug report. If you could send a file that demonstrates the problem, that would be very helpful. You can upload files here: http://qa.openmicroscopy.org.uk/qa/upload/ If that doesn't work, please let us know and we'll send alternate upload instructions. Regards, -Melissa P.S. For future, it is best to send questions like this to the ome-users mailing list (in CC), as that ensures a prompt reply even if I am away. On Wed, Feb 13, 2013 at 12:01:54PM -0800, Henry Pinkard wrote: > Hi Melissa, > > I was wondering if you all are aware of the bug reading nd2 files created > by the most recent version of Nikon Elements with loci_tools.jar 4.4.6? > When I try to open an nd2, I get the stack trace below. Do you know if this > is fixable/if there is some kind of workaround? I'm happy to send you a > test file if you need. > > Best, > Henry > > > java.lang.IllegalArgumentException: 0 must not be null and positive. > at ome.xml.model.primitives.PositiveInteger.(PositiveInteger.java:56) > at loci.formats.MetadataTools.populatePixelsOnly(MetadataTools.java:266) > at loci.formats.MetadataTools.populatePixelsOnly(MetadataTools.java:240) > at loci.formats.ChannelFiller.setId(ChannelFiller.java:267) > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529) > at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274) > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529) > at loci.formats.DimensionSwapper.setId(DimensionSwapper.java:292) > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529) > at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529) > at loci.plugins.in.ImportProcess.setId(ImportProcess.java:685) > at loci.plugins.in.ImportProcess.initializeStack(ImportProcess.java:522) > at loci.plugins.in.ImportProcess.execute(ImportProcess.java:150) > at loci.plugins.in.Importer.showDialogs(Importer.java:141) > at loci.plugins.in.Importer.run(Importer.java:79) > at loci.plugins.LociImporter.run(LociImporter.java:81) > at ij.IJ.runUserPlugIn(IJ.java:185) > at ij.IJ.runPlugIn(IJ.java:152) > at ij.Executer.runCommand(Executer.java:127) > at ij.Executer.run(Executer.java:64) > at java.lang.Thread.run(Thread.java:662) From P.Thomas at uea.ac.uk Thu Feb 14 09:13:12 2013 From: P.Thomas at uea.ac.uk (Paul Thomas (BIO)) Date: Thu, 14 Feb 2013 09:13:12 +0000 Subject: [ome-users] ImSpectorPro support Message-ID: <813C5441A8B6B5439711C30EB6A9EB50049538@ueastfexch01.UEA.AC.UK> I have a multi-photon microscope from LaVision Biotec that generates files with the extension *.msr. Presently, import of these files into ImageJ is not supported by Bioformats. Is there any ongoing effort to change this situation, or has no-one expressed an interest in this file format, or has someone tried and failed? Several of my users would be very happy if we could open these files in ImageJ. I can provide example files if that would help. Paul Thomas. -------------- next part -------------- An HTML attachment was scrubbed... URL: From philippe.mailly at snv.jussieu.fr Thu Feb 14 10:56:14 2013 From: philippe.mailly at snv.jussieu.fr (Philippe Mailly) Date: Thu, 14 Feb 2013 11:56:14 +0100 Subject: [ome-users] The OMERO cpp libraries Message-ID: <511CC2CE.5070607@snv.jussieu.fr> Hi, I'm trying to complile -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: philippe_mailly.vcf Type: text/x-vcard Size: 364 bytes Desc: not available URL: From philippe.mailly at snv.jussieu.fr Thu Feb 14 11:03:36 2013 From: philippe.mailly at snv.jussieu.fr (Philippe Mailly) Date: Thu, 14 Feb 2013 12:03:36 +0100 Subject: [ome-users] The OMERO cpp libraries Message-ID: <511CC488.8080803@snv.jussieu.fr> Hi, I'm trying to compile The OMERO cpp libraries, on Ubuntu 12.10 to install volviewer with omero server support. the build with ./build.py is fine, however ./build.py build-cpp return a message concerning the ICE.h Entering /home/phm/Developpement/openmicroscopy/components/tools/OmeroCpp... build: Building with ICE_HOME=/usr/include Debug setting: True (debug) 64-Bit build: True (detect) Ice/Ice.h not found I have Ice libdev installed [phm at phm-X8DAL:~/Developpement/openmicroscopy]$ locate Ice.h /home/phm/Developpement/openmicroscopy/target/Ice/include/Ice/._Ice.h /home/phm/Developpement/openmicroscopy/target/Ice/include/Ice/Ice.h /usr/include/Ice/Ice.h /usr/share/doc/ice34-slice/reference/Ice.html export ICE_HOME=/home/phm/Developpement/openmicroscopy/target/Ice/include give the same result Any suggestions Philippe -------------- next part -------------- A non-text attachment was scrubbed... Name: philippe_mailly.vcf Type: text/x-vcard Size: 364 bytes Desc: not available URL: From josh at glencoesoftware.com Thu Feb 14 12:14:14 2013 From: josh at glencoesoftware.com (Josh Moore) Date: Thu, 14 Feb 2013 13:14:14 +0100 Subject: [ome-users] The OMERO cpp libraries In-Reply-To: <511CC488.8080803@snv.jussieu.fr> References: <511CC488.8080803@snv.jussieu.fr> Message-ID: <4810CA84-7BF9-424A-805E-3B4C98ECD64E@glencoesoftware.com> On Feb 14, 2013, at 12:03 PM, Philippe Mailly wrote: > Hi, Hi Philippe, > I'm trying to compile The OMERO cpp libraries, on Ubuntu 12.10 to install volviewer with omero server support. > > the build with ./build.py is fine, however ./build.py build-cpp return a message concerning the ICE.h > > Entering /home/phm/Developpement/openmicroscopy/components/tools/OmeroCpp... > > build: > Building with ICE_HOME=/usr/include > Debug setting: True (debug) > 64-Bit build: True (detect) > Ice/Ice.h not found > > I have Ice libdev installed > > [phm at phm-X8DAL:~/Developpement/openmicroscopy]$ locate Ice.h > /home/phm/Developpement/openmicroscopy/target/Ice/include/Ice/._Ice.h > /home/phm/Developpement/openmicroscopy/target/Ice/include/Ice/Ice.h > /usr/include/Ice/Ice.h > /usr/share/doc/ice34-slice/reference/Ice.html > > export ICE_HOME=/home/phm/Developpement/openmicroscopy/target/Ice/include > give the same result Can you take a look at and/or send the contents of components/tools/OmeroCpp/.sconf_temp/? Cheers, ~Josh. > Any suggestions > Philippe From josh at glencoesoftware.com Thu Feb 14 14:53:32 2013 From: josh at glencoesoftware.com (Josh Moore) Date: Thu, 14 Feb 2013 15:53:32 +0100 Subject: [ome-users] The OMERO cpp libraries In-Reply-To: <511CDF66.4080503@snv.jussieu.fr> References: <511CC488.8080803@snv.jussieu.fr> <4810CA84-7BF9-424A-805E-3B4C98ECD64E@glencoesoftware.com> <511CDF66.4080503@snv.jussieu.fr> Message-ID: On Feb 14, 2013, at 1:58 PM, Philippe Mailly wrote: > Hi Josh, Hi Philippe, > in components/tools/OmeroCpp/.sconf_temp/ have one file conftest_O.cpp > with > > #include "Ice/Ice.h" Can you use the CPPPATH environment variable to pass your includes location? See https://www.openmicroscopy.org/site/support/omero4/developers/Cpp.html for more info. Cheers, ~Josh. > Philippe > > Le 14/02/2013 13:14, Josh Moore a ?crit : >> On Feb 14, 2013, at 12:03 PM, Philippe Mailly wrote: >> >>> Hi, >> Hi Philippe, >> >>> I'm trying to compile The OMERO cpp libraries, on Ubuntu 12.10 to install volviewer with omero server support. >>> >>> the build with ./build.py is fine, however ./build.py build-cpp return a message concerning the ICE.h >>> >>> Entering /home/phm/Developpement/openmicroscopy/components/tools/OmeroCpp... >>> >>> build: >>> Building with ICE_HOME=/usr/include >>> Debug setting: True (debug) >>> 64-Bit build: True (detect) >>> Ice/Ice.h not found >>> >>> I have Ice libdev installed >>> >>> [phm at phm-X8DAL:~/Developpement/openmicroscopy]$ locate Ice.h >>> /home/phm/Developpement/openmicroscopy/target/Ice/include/Ice/._Ice.h >>> /home/phm/Developpement/openmicroscopy/target/Ice/include/Ice/Ice.h >>> /usr/include/Ice/Ice.h >>> /usr/share/doc/ice34-slice/reference/Ice.html >>> >>> export ICE_HOME=/home/phm/Developpement/openmicroscopy/target/Ice/include >>> give the same result >> Can you take a look at and/or send the contents of components/tools/OmeroCpp/.sconf_temp/? >> >> Cheers, >> ~Josh. >> >> >>> Any suggestions >>> Philippe >> > > From j.burel at dundee.ac.uk Thu Feb 14 15:54:52 2013 From: j.burel at dundee.ac.uk (Jean-Marie Burel) Date: Thu, 14 Feb 2013 15:54:52 +0000 Subject: [ome-users] ImSpectorPro support In-Reply-To: <813C5441A8B6B5439711C30EB6A9EB50049538@ueastfexch01.UEA.AC.UK> Message-ID: Dear Paul Thanks for your interest. The format is not supported and we have not yet discussed adding support for it but we will certainly be interested with sample data. Other institutions have expressed similar interest. You should have an option to save the file as an OME-TIFF instead of the proprietary format, you will then be able to open the images using Bioformats Regards Jmarie The University of Dundee is a registered Scottish Charity, No: SC015096 -------------- next part -------------- An HTML attachment was scrubbed... URL: From P.Thomas at uea.ac.uk Thu Feb 14 15:58:10 2013 From: P.Thomas at uea.ac.uk (Paul Thomas (BIO)) Date: Thu, 14 Feb 2013 15:58:10 +0000 Subject: [ome-users] ImSpectorPro support In-Reply-To: References: <813C5441A8B6B5439711C30EB6A9EB50049538@ueastfexch01.UEA.AC.UK> Message-ID: <813C5441A8B6B5439711C30EB6A9EB500497C6@ueastfexch01.UEA.AC.UK> Hi Jmarie, We already use the export to ome.tif and then open in ImageJ, but it is just one more step to carry out. I've already uploaded some example images to your "trac" site. Thanks, Paul. ____________________ Dr. Paul Thomas, Director, The Henry Wellcome Laboratory for Cell Imaging, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom. e-mail: p.thomas at uea.ac.uk Tel: +44-1603-592196 Fax: +44-1603-592250 Imaging web-site: https://lred.uea.ac.uk/web/henry-wellcome-laboratory-for-cell-imaging/welcome Personal web-page: http://biobis.bio.uea.ac.uk/biosql/fac_show.aspx?ID=548 From: Jean-Marie Burel [mailto:j.burel at dundee.ac.uk] Sent: 14 February 2013 15:55 To: Paul Thomas (BIO); ome-users at lists.openmicroscopy.org.uk Subject: Re: [ome-users] ImSpectorPro support Dear Paul Thanks for your interest. The format is not supported and we have not yet discussed adding support for it but we will certainly be interested with sample data. Other institutions have expressed similar interest. You should have an option to save the file as an OME-TIFF instead of the proprietary format, you will then be able to open the images using Bioformats Regards Jmarie The University of Dundee is a registered Scottish Charity, No: SC015096 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jesse at glencoesoftware.com Thu Feb 14 18:19:57 2013 From: jesse at glencoesoftware.com (Jesse Corrington) Date: Thu, 14 Feb 2013 10:19:57 -0800 Subject: [ome-users] The OMERO cpp libraries In-Reply-To: References: <511CC488.8080803@snv.jussieu.fr> <4810CA84-7BF9-424A-805E-3B4C98ECD64E@glencoesoftware.com> <511CDF66.4080503@snv.jussieu.fr> Message-ID: Hi Philippe, If you have ICE_HOME set correctly, and you've tried Josh's CPPPATH suggestion, the problem may be that scons has incorrect settings for your c++ compiler for some reason. The error, "Ice.h not found" is a little misleading, because it simply means scons failed to build a sample c++ file that includes Ice.h. It could also mean that either your systems c++ compiler isn't' setup properly, or for some reason scons is not using the correct compiler. I saw this problem when I accidentally had my CXX environment variable set to empty string. Our scons build script was overriding the scons CXX variable with mine, which was empty string. If you happen to have this same problem, doing "unset CXX" before building should fix the problem. Otherwise, there's probably a different issue with scons finding your compiler or your compiler isn't working. You should have a look at compiler.log that is created in the components/tools/OmeroCpp directory that has information about what compiler and flags scons is trying use and make sure it looks correct. I'll be making some changes today to the scons build script to better report errors in situations like this. Jesse On Feb 14, 2013, at 6:53 AM, Josh Moore wrote: > > On Feb 14, 2013, at 1:58 PM, Philippe Mailly wrote: > >> Hi Josh, > > Hi Philippe, > >> in components/tools/OmeroCpp/.sconf_temp/ have one file conftest_O.cpp >> with >> >> #include "Ice/Ice.h" > > Can you use the CPPPATH environment variable to pass your includes location? > > See https://www.openmicroscopy.org/site/support/omero4/developers/Cpp.html for more info. > > Cheers, > ~Josh. > > > >> Philippe >> >> Le 14/02/2013 13:14, Josh Moore a ?crit : >>> On Feb 14, 2013, at 12:03 PM, Philippe Mailly wrote: >>> >>>> Hi, >>> Hi Philippe, >>> >>>> I'm trying to compile The OMERO cpp libraries, on Ubuntu 12.10 to install volviewer with omero server support. >>>> >>>> the build with ./build.py is fine, however ./build.py build-cpp return a message concerning the ICE.h >>>> >>>> Entering /home/phm/Developpement/openmicroscopy/components/tools/OmeroCpp... >>>> >>>> build: >>>> Building with ICE_HOME=/usr/include >>>> Debug setting: True (debug) >>>> 64-Bit build: True (detect) >>>> Ice/Ice.h not found >>>> >>>> I have Ice libdev installed >>>> >>>> [phm at phm-X8DAL:~/Developpement/openmicroscopy]$ locate Ice.h >>>> /home/phm/Developpement/openmicroscopy/target/Ice/include/Ice/._Ice.h >>>> /home/phm/Developpement/openmicroscopy/target/Ice/include/Ice/Ice.h >>>> /usr/include/Ice/Ice.h >>>> /usr/share/doc/ice34-slice/reference/Ice.html >>>> >>>> export ICE_HOME=/home/phm/Developpement/openmicroscopy/target/Ice/include >>>> give the same result >>> Can you take a look at and/or send the contents of components/tools/OmeroCpp/.sconf_temp/? >>> >>> Cheers, >>> ~Josh. >>> >>> >>>> Any suggestions >>>> Philippe >>> >> >> > > _______________________________________________ > ome-users mailing list > ome-users at lists.openmicroscopy.org.uk > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users From a.smith at centenary.org.au Thu Feb 14 22:42:43 2013 From: a.smith at centenary.org.au (Adrian Smith) Date: Fri, 15 Feb 2013 09:42:43 +1100 Subject: [ome-users] ImSpectorPro support In-Reply-To: <813C5441A8B6B5439711C30EB6A9EB500497C6@ueastfexch01.UEA.AC.UK> References: <813C5441A8B6B5439711C30EB6A9EB50049538@ueastfexch01.UEA.AC.UK> <813C5441A8B6B5439711C30EB6A9EB500497C6@ueastfexch01.UEA.AC.UK> Message-ID: Hi all, We also have three TriMScope's here at the Centenary Institute and would be very interested in .msr support in Bioformats. As noted we do use the OME-TIFF export but direct access would be an advantage. Regards, Adrian Smith Centenary Institute, Sydney, Australia On 15/02/2013, at 2:58 AM, "Paul Thomas (BIO)" wrote: > Hi Jmarie, > We already use the export to ome.tif and then open in ImageJ, but it is just one more step to carry out. I?ve already uploaded some example images to your ?trac? site. > Thanks, > Paul. > ____________________ > Dr. Paul Thomas, Director, > The Henry Wellcome Laboratory for Cell Imaging, > School of Biological Sciences, > University of East Anglia, > Norwich Research Park, > Norwich, > NR4 7TJ, > United Kingdom. > > e-mail: p.thomas at uea.ac.uk > Tel: +44-1603-592196 > Fax: +44-1603-592250 > Imaging web-site: https://lred.uea.ac.uk/web/henry-wellcome-laboratory-for-cell-imaging/welcome > Personal web-page: http://biobis.bio.uea.ac.uk/biosql/fac_show.aspx?ID=548 > > From: Jean-Marie Burel [mailto:j.burel at dundee.ac.uk] > Sent: 14 February 2013 15:55 > To: Paul Thomas (BIO); ome-users at lists.openmicroscopy.org.uk > Subject: Re: [ome-users] ImSpectorPro support > > Dear Paul > > Thanks for your interest. > > The format is not supported and we have not yet discussed adding support for it but we will certainly be interested with sample data. > Other institutions have expressed similar interest. > > You should have an option to save the file as an OME-TIFF instead of the proprietary format, you will then be able to open the images using Bioformats > > Regards > > Jmarie > > > > The University of Dundee is a registered Scottish Charity, No: SC015096 > _______________________________________________ > ome-users mailing list > ome-users at lists.openmicroscopy.org.uk > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From philippe.mailly at snv.jussieu.fr Fri Feb 15 10:44:37 2013 From: philippe.mailly at snv.jussieu.fr (Philippe Mailly) Date: Fri, 15 Feb 2013 11:44:37 +0100 Subject: [ome-users] The OMERO cpp libraries In-Reply-To: References: <511CC488.8080803@snv.jussieu.fr> <4810CA84-7BF9-424A-805E-3B4C98ECD64E@glencoesoftware.com> <511CDF66.4080503@snv.jussieu.fr>

Message-ID: <511E1195.5040403@snv.jussieu.fr> Hi Jesse and Josh, I had tried all suggested options without success. export CPPPATH=/usr/include/Ice same error about Ice.h if I unset CXX I got more errors A lot of something like : Compiling src/omero/model/DetailsI.os sh: 1: o: not found ....... and at this end : Install file: "libomero_client.so" as "target/lib/libomero_client.so" scons: *** [target/lib/libomero_client.so] libomero_client.so: No such file or directory the compiling.log with CXX unset: # # Scons Compile Log : Fri Feb 15 11:39:07 2013 # CXXFLAGS=-Wall -ansi -Wno-long-long -Wnon-virtual-dtor -Wno-unused-parameter -Wno-unused-function -Wunused-variable -Wunused-value -O0 - g CPPPATH=['src', 'target', '/home/phm/Developpement/openmicroscopy/components/blitz/generated', '/usr/include/Ice', '/home/phm/Developpem ent/openmicroscopy/target/Ice/include'] CXX=gcc CXXVERSION=4.7.2 LIBPATH=['/home/phm/Developpement/openmicroscopy/components/tools/OmeroCpp', '/home/phm/Developpement/openmicroscopy/target/Ice/lib'] ARCH=64 RELEASE=dbg PLATFORM=posix I have gcc install and working (i did some other compilations without any problem) I can try with Intel compiler which is also on my machine ? Philippe Le 14/02/2013 19:19, Jesse Corrington a ?crit : > Hi Philippe, > > If you have ICE_HOME set correctly, and you've tried Josh's CPPPATH suggestion, the problem may be that scons has incorrect settings for your c++ compiler for some reason. The error, "Ice.h not found" is a little misleading, because it simply means scons failed to build a sample c++ file that includes Ice.h. It could also mean that either your systems c++ compiler isn't' setup properly, or for some reason scons is not using the correct compiler. I saw this problem when I accidentally had my CXX environment variable set to empty string. Our scons build script was overriding the scons CXX variable with mine, which was empty string. If you happen to have this same problem, doing "unset CXX" before building should fix the problem. Otherwise, there's probably a different issue with scons finding your compiler or your compiler isn't working. You should have a look at compiler.log that is created in the components/tools/OmeroCpp directory that has information about what compiler and flags scons is trying use and make sure it looks correct. I'll be making some changes today to the scons build script to better report errors in situations like this. > > Jesse > > On Feb 14, 2013, at 6:53 AM, Josh Moore wrote: > >> On Feb 14, 2013, at 1:58 PM, Philippe Mailly wrote: >> >>> Hi Josh, >> Hi Philippe, >> >>> in components/tools/OmeroCpp/.sconf_temp/ have one file conftest_O.cpp >>> with >>> >>> #include "Ice/Ice.h" >> Can you use the CPPPATH environment variable to pass your includes location? >> >> See https://www.openmicroscopy.org/site/support/omero4/developers/Cpp.html for more info. >> >> Cheers, >> ~Josh. >> >> >> >>> Philippe >>> >>> Le 14/02/2013 13:14, Josh Moore a ?crit : >>>> On Feb 14, 2013, at 12:03 PM, Philippe Mailly wrote: >>>> >>>>> Hi, >>>> Hi Philippe, >>>> >>>>> I'm trying to compile The OMERO cpp libraries, on Ubuntu 12.10 to install volviewer with omero server support. >>>>> >>>>> the build with ./build.py is fine, however ./build.py build-cpp return a message concerning the ICE.h >>>>> >>>>> Entering /home/phm/Developpement/openmicroscopy/components/tools/OmeroCpp... >>>>> >>>>> build: >>>>> Building with ICE_HOME=/usr/include >>>>> Debug setting: True (debug) >>>>> 64-Bit build: True (detect) >>>>> Ice/Ice.h not found >>>>> >>>>> I have Ice libdev installed >>>>> >>>>> [phm at phm-X8DAL:~/Developpement/openmicroscopy]$ locate Ice.h >>>>> /home/phm/Developpement/openmicroscopy/target/Ice/include/Ice/._Ice.h >>>>> /home/phm/Developpement/openmicroscopy/target/Ice/include/Ice/Ice.h >>>>> /usr/include/Ice/Ice.h >>>>> /usr/share/doc/ice34-slice/reference/Ice.html >>>>> >>>>> export ICE_HOME=/home/phm/Developpement/openmicroscopy/target/Ice/include >>>>> give the same result >>>> Can you take a look at and/or send the contents of components/tools/OmeroCpp/.sconf_temp/? >>>> >>>> Cheers, >>>> ~Josh. >>>> >>>> >>>>> Any suggestions >>>>> Philippe >>> >> _______________________________________________ >> ome-users mailing list >> ome-users at lists.openmicroscopy.org.uk >> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users > -------------- next part -------------- A non-text attachment was scrubbed... Name: philippe_mailly.vcf Type: text/x-vcard Size: 364 bytes Desc: not available URL: From josh at glencoesoftware.com Fri Feb 15 10:45:01 2013 From: josh at glencoesoftware.com (Josh Moore) Date: Fri, 15 Feb 2013 11:45:01 +0100 Subject: [ome-users] The OMERO cpp libraries In-Reply-To: <511E1195.5040403@snv.jussieu.fr> References: <511CC488.8080803@snv.jussieu.fr> <4810CA84-7BF9-424A-805E-3B4C98ECD64E@glencoesoftware.com> <511CDF66.4080503@snv.jussieu.fr>

<511E1195.5040403@snv.jussieu.fr> Message-ID: On Feb 15, 2013, at 11:44 AM, Philippe Mailly wrote: > Hi Jesse and Josh, Hi Philippe, > I had tried all suggested options without success. > export CPPPATH=/usr/include/Ice > same error about Ice.h > > if I unset CXX > I got more errors > A lot of something like : > > Compiling src/omero/model/DetailsI.os > sh: 1: o: not found > ....... > and at this end : > > Install file: "libomero_client.so" as "target/lib/libomero_client.so" > scons: *** [target/lib/libomero_client.so] libomero_client.so: No such file or directory Can you try setting the following: export CPPPATH=/usr/include export CXX=g++ export VERBOSE=1 Thanks, ~Josh. > the compiling.log with CXX unset: > # > # Scons Compile Log : Fri Feb 15 11:39:07 2013 > # > CXXFLAGS=-Wall -ansi -Wno-long-long -Wnon-virtual-dtor -Wno-unused-parameter -Wno-unused-function -Wunused-variable -Wunused-value -O0 - > g > CPPPATH=['src', 'target', '/home/phm/Developpement/openmicroscopy/components/blitz/generated', '/usr/include/Ice', '/home/phm/Developpem > ent/openmicroscopy/target/Ice/include'] > CXX=gcc > CXXVERSION=4.7.2 > LIBPATH=['/home/phm/Developpement/openmicroscopy/components/tools/OmeroCpp', '/home/phm/Developpement/openmicroscopy/target/Ice/lib'] > ARCH=64 > RELEASE=dbg > PLATFORM=posix > > I have gcc install and working (i did some other compilations without any problem) > I can try with Intel compiler which is also on my machine ? > > Philippe > > Le 14/02/2013 19:19, Jesse Corrington a ?crit : >> Hi Philippe, >> >> If you have ICE_HOME set correctly, and you've tried Josh's CPPPATH suggestion, the problem may be that scons has incorrect settings for your c++ compiler for some reason. The error, "Ice.h not found" is a little misleading, because it simply means scons failed to build a sample c++ file that includes Ice.h. It could also mean that either your systems c++ compiler isn't' setup properly, or for some reason scons is not using the correct compiler. I saw this problem when I accidentally had my CXX environment variable set to empty string. Our scons build script was overriding the scons CXX variable with mine, which was empty string. If you happen to have this same problem, doing "unset CXX" before building should fix the problem. Otherwise, there's probably a different issue with scons finding your compiler or your compiler isn't working. You should have a look at compiler.log that is created in the components/tools/OmeroCpp directory that has information about what compiler and flags scons is trying use and make sure it looks correct. I'll be making some changes today to the scons build script to better report errors in situations like this. >> >> Jesse >> >> On Feb 14, 2013, at 6:53 AM, Josh Moore wrote: >> >>> On Feb 14, 2013, at 1:58 PM, Philippe Mailly wrote: >>> >>>> Hi Josh, >>> Hi Philippe, >>> >>>> in components/tools/OmeroCpp/.sconf_temp/ have one file conftest_O.cpp >>>> with >>>> >>>> #include "Ice/Ice.h" >>> Can you use the CPPPATH environment variable to pass your includes location? >>> >>> See https://www.openmicroscopy.org/site/support/omero4/developers/Cpp.html for more info. >>> >>> Cheers, >>> ~Josh. >>> >>> >>> >>>> Philippe >>>> >>>> Le 14/02/2013 13:14, Josh Moore a ?crit : >>>>> On Feb 14, 2013, at 12:03 PM, Philippe Mailly wrote: >>>>> >>>>>> Hi, >>>>> Hi Philippe, >>>>> >>>>>> I'm trying to compile The OMERO cpp libraries, on Ubuntu 12.10 to install volviewer with omero server support. >>>>>> >>>>>> the build with ./build.py is fine, however ./build.py build-cpp return a message concerning the ICE.h >>>>>> >>>>>> Entering /home/phm/Developpement/openmicroscopy/components/tools/OmeroCpp... >>>>>> >>>>>> build: >>>>>> Building with ICE_HOME=/usr/include >>>>>> Debug setting: True (debug) >>>>>> 64-Bit build: True (detect) >>>>>> Ice/Ice.h not found >>>>>> >>>>>> I have Ice libdev installed >>>>>> >>>>>> [phm at phm-X8DAL:~/Developpement/openmicroscopy]$ locate Ice.h >>>>>> /home/phm/Developpement/openmicroscopy/target/Ice/include/Ice/._Ice.h >>>>>> /home/phm/Developpement/openmicroscopy/target/Ice/include/Ice/Ice.h >>>>>> /usr/include/Ice/Ice.h >>>>>> /usr/share/doc/ice34-slice/reference/Ice.html >>>>>> >>>>>> export ICE_HOME=/home/phm/Developpement/openmicroscopy/target/Ice/include >>>>>> give the same result >>>>> Can you take a look at and/or send the contents of components/tools/OmeroCpp/.sconf_temp/? >>>>> >>>>> Cheers, >>>>> ~Josh. From m.woodbridge at imperial.ac.uk Fri Feb 15 11:29:01 2013 From: m.woodbridge at imperial.ac.uk (Mark Woodbridge) Date: Fri, 15 Feb 2013 11:29:01 +0000 Subject: [ome-users] Publishing images using OMERO Message-ID: <511E1BFD.8010509@imperial.ac.uk> Hi, In case anyone has experience of publishing images using OMERO but isn't a regular on the forums... it would be useful to hear your experiences: http://www.openmicroscopy.org/community/viewtopic.php?f=4&t=4460 Thanks, Mark. From josh at glencoesoftware.com Fri Feb 15 18:29:34 2013 From: josh at glencoesoftware.com (Josh Moore) Date: Fri, 15 Feb 2013 19:29:34 +0100 Subject: [ome-users] ImSpectorPro support In-Reply-To: References: <813C5441A8B6B5439711C30EB6A9EB50049538@ueastfexch01.UEA.AC.UK> <813C5441A8B6B5439711C30EB6A9EB500497C6@ueastfexch01.UEA.AC.UK> Message-ID: <20499237-98F9-4649-AAD2-68C9CA8F8B98@glencoesoftware.com> On Feb 14, 2013, at 11:42 PM, Adrian Smith wrote: > Hi all, Hello, There's currently a ticket on our trac: http://trac.openmicroscopy.org.uk/ome/ticket/8071 If you would like to be CC'd, please let us know. Sample data is always appreciated. Cheers, ~Josh > We also have three TriMScope's here at the Centenary Institute and would be very interested in .msr support in Bioformats. > > As noted we do use the OME-TIFF export but direct access would be an advantage. > > Regards, > > Adrian Smith > Centenary Institute, Sydney, Australia > > > On 15/02/2013, at 2:58 AM, "Paul Thomas (BIO)" wrote: > >> Hi Jmarie, >> We already use the export to ome.tif and then open in ImageJ, but it is just one more step to carry out. I?ve already uploaded some example images to your ?trac? site. >> Thanks, >> Paul. >> ____________________ >> Dr. Paul Thomas, Director, >> The Henry Wellcome Laboratory for Cell Imaging, >> School of Biological Sciences, >> University of East Anglia, >> Norwich Research Park, >> Norwich, >> NR4 7TJ, >> United Kingdom. >> >> e-mail: p.thomas at uea.ac.uk >> Tel: +44-1603-592196 >> Fax: +44-1603-592250 >> Imaging web-site: https://lred.uea.ac.uk/web/henry-wellcome-laboratory-for-cell-imaging/welcome >> Personal web-page: http://biobis.bio.uea.ac.uk/biosql/fac_show.aspx?ID=548 >> >> From: Jean-Marie Burel [mailto:j.burel at dundee.ac.uk] >> Sent: 14 February 2013 15:55 >> To: Paul Thomas (BIO); ome-users at lists.openmicroscopy.org.uk >> Subject: Re: [ome-users] ImSpectorPro support >> >> Dear Paul >> >> Thanks for your interest. >> >> The format is not supported and we have not yet discussed adding support for it but we will certainly be interested with sample data. >> Other institutions have expressed similar interest. >> >> You should have an option to save the file as an OME-TIFF instead of the proprietary format, you will then be able to open the images using Bioformats >> >> Regards >> >> Jmarie >> >> >> >> The University of Dundee is a registered Scottish Charity, No: SC015096 >> _______________________________________________ >> ome-users mailing list >> ome-users at lists.openmicroscopy.org.uk >> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users > > _______________________________________________ > ome-users mailing list > ome-users at lists.openmicroscopy.org.uk > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users From r.leigh at dundee.ac.uk Fri Feb 15 21:49:43 2013 From: r.leigh at dundee.ac.uk (Roger Leigh) Date: Fri, 15 Feb 2013 21:49:43 +0000 Subject: [ome-users] The OMERO cpp libraries In-Reply-To: References: <511CC488.8080803@snv.jussieu.fr> <4810CA84-7BF9-424A-805E-3B4C98ECD64E@glencoesoftware.com> <511CDF66.4080503@snv.jussieu.fr>

<511E1195.5040403@snv.jussieu.fr> Message-ID: <511EAD77.8040709@dundee.ac.uk> On 15/02/2013 10:45, Josh Moore wrote: > > On Feb 15, 2013, at 11:44 AM, Philippe Mailly wrote: > >> Hi Jesse and Josh, > > Hi Philippe, > >> I had tried all suggested options without success. >> export CPPPATH=/usr/include/Ice >> same error about Ice.h >> >> if I unset CXX >> I got more errors >> A lot of something like : >> >> Compiling src/omero/model/DetailsI.os >> sh: 1: o: not found >> ....... >> and at this end : >> >> Install file: "libomero_client.so" as "target/lib/libomero_client.so" >> scons: *** [target/lib/libomero_client.so] libomero_client.so: No such file or directory > > Can you try setting the following: > > export CPPPATH=/usr/include > export CXX=g++ > export VERBOSE=1 The problem here is most likely using the default system compiler, which chokes on the broken Ice headers. This is what causes the Ice/Ice.h not found error (the diagnostic here is poor--the header does exist, but the test for it fails because the header is not valid C++, and newer GCC versions have stricter C++ syntax checking). If you look with the verbose logging, you'll probably see that g++ errors out. If you install g++-4.4 and try building with CXX=g++-4.4 you might have a little more success. Not ideal, but Ice is broken and that's currently the only option. Regards, Roger -- Dr Roger Leigh -- Open Microscopy Environment Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH Scotland UK Tel: (01382) 386364 The University of Dundee is a registered Scottish Charity, No: SC015096 From bongiornot at gmail.com Sat Feb 16 16:24:41 2013 From: bongiornot at gmail.com (Tom Bongiorno) Date: Sat, 16 Feb 2013 11:24:41 -0500 Subject: [ome-users] Bio-Formats ImageJ bit depth Message-ID: Hello, I am using the Bio-Formats plugin on ImageJ to import JPEG2000 images. Although all the images are 16-bit, when using the "Measure" command, the dynamic range of the mean pixel value seems to be variable (i.e. dependent on the particular image). If I select part of my image and run the "Fill" command (to get a black square), the mean pixel value will be 0. But when I run the "Invert" command on the filled region (to get a white square), the mean pixel value is inconsistent (I'd expect 65535). Some values I've gotten are 1757, 2449, 6832, and 7902. Any assistance or explanation would be greatly appreciated. Tom Georgia Tech -------------- next part -------------- An HTML attachment was scrubbed... URL: From l.bugnon at gmail.com Sun Feb 17 23:28:33 2013 From: l.bugnon at gmail.com (Leandro Bugnon) Date: Sun, 17 Feb 2013 20:28:33 -0300 Subject: [ome-users] OME-XML File Message-ID: Dear developers, I need to write a file with metadata only (OME-XML) for configuration purposes. What class could I use to do this?. IFileWriter asks me an image, but i only need the metadata. Thank you very much. Best Regards, -- Leandro -------------- next part -------------- An HTML attachment was scrubbed... URL: From philippe.mailly at snv.jussieu.fr Mon Feb 18 08:51:34 2013 From: philippe.mailly at snv.jussieu.fr (Philippe Mailly) Date: Mon, 18 Feb 2013 09:51:34 +0100 Subject: [ome-users] The OMERO cpp libraries In-Reply-To: <511EAD77.8040709@dundee.ac.uk> References: <511CC488.8080803@snv.jussieu.fr> <4810CA84-7BF9-424A-805E-3B4C98ECD64E@glencoesoftware.com> <511CDF66.4080503@snv.jussieu.fr>

<511E1195.5040403@snv.jussieu.fr> <511EAD77.8040709@dundee.ac.uk> Message-ID: <5121EB96.5070102@snv.jussieu.fr> Thanks a lot Roger, with g++-4.4 compilation is successful : BUILD SUCCESSFUL Total time: 22 minutes 13 seconds May be the problem of gcc version is the same as python version. On a Mac compilation fail quickly with python version 3.xx Philippe Le 15/02/2013 22:49, Roger Leigh a ?crit : > On 15/02/2013 10:45, Josh Moore wrote: >> >> On Feb 15, 2013, at 11:44 AM, Philippe Mailly wrote: >> >>> Hi Jesse and Josh, >> >> Hi Philippe, >> >>> I had tried all suggested options without success. >>> export CPPPATH=/usr/include/Ice >>> same error about Ice.h >>> >>> if I unset CXX >>> I got more errors >>> A lot of something like : >>> >>> Compiling src/omero/model/DetailsI.os >>> sh: 1: o: not found >>> ....... >>> and at this end : >>> >>> Install file: "libomero_client.so" as "target/lib/libomero_client.so" >>> scons: *** [target/lib/libomero_client.so] libomero_client.so: No >>> such file or directory >> >> Can you try setting the following: >> >> export CPPPATH=/usr/include >> export CXX=g++ >> export VERBOSE=1 > > The problem here is most likely using the default system compiler, which > chokes on the broken Ice headers. This is what causes the Ice/Ice.h not > found error (the diagnostic here is poor--the header does exist, but the > test for it fails because the header is not valid C++, and newer GCC > versions have stricter C++ syntax checking). If you look with the > verbose logging, you'll probably see that g++ errors out. > > If you install g++-4.4 and try building with > CXX=g++-4.4 > you might have a little more success. Not ideal, but Ice is broken and > that's currently the only option. > > > Regards, > Roger > > -- > Dr Roger Leigh -- Open Microscopy Environment > Wellcome Trust Centre for Gene Regulation and Expression, > College of Life Sciences, University of Dundee, Dow Street, > Dundee DD1 5EH Scotland UK Tel: (01382) 386364 > > The University of Dundee is a registered Scottish Charity, No: SC015096 > > -------------- next part -------------- A non-text attachment was scrubbed... Name: philippe_mailly.vcf Type: text/x-vcard Size: 364 bytes Desc: not available URL: From josh at glencoesoftware.com Mon Feb 18 09:03:50 2013 From: josh at glencoesoftware.com (Josh Moore) Date: Mon, 18 Feb 2013 10:03:50 +0100 Subject: [ome-users] The OMERO cpp libraries In-Reply-To: <5121EB96.5070102@snv.jussieu.fr> References: <511CC488.8080803@snv.jussieu.fr> <4810CA84-7BF9-424A-805E-3B4C98ECD64E@glencoesoftware.com> <511CDF66.4080503@snv.jussieu.fr>

<511E1195.5040403@snv.jussieu.fr> <511EAD77.8040709@dundee.ac.uk> <5121EB96.5070102@snv.jussieu.fr> Message-ID: <52E3E2D7-334F-4B10-AFDF-C7F480D4B61B@glencoesoftware.com> Hi Philippe, On Feb 18, 2013, at 9:51 AM, Philippe Mailly wrote: > Thanks a lot Roger, with g++-4.4 compilation is successful : > > BUILD SUCCESSFUL > Total time: 22 minutes 13 seconds > > May be the problem of gcc version is the same as python version. On a Mac compilation fail quickly with python version 3.xx Ice does not support Python 3.x at the moment, so this is likely the same problem. Cheers, ~Josh. > Philippe > > Le 15/02/2013 22:49, Roger Leigh a ?crit : >> On 15/02/2013 10:45, Josh Moore wrote: >>> >>> On Feb 15, 2013, at 11:44 AM, Philippe Mailly wrote: >>> >>>> Hi Jesse and Josh, >>> >>> Hi Philippe, >>> >>>> I had tried all suggested options without success. >>>> export CPPPATH=/usr/include/Ice >>>> same error about Ice.h >>>> >>>> if I unset CXX >>>> I got more errors >>>> A lot of something like : >>>> >>>> Compiling src/omero/model/DetailsI.os >>>> sh: 1: o: not found >>>> ....... >>>> and at this end : >>>> >>>> Install file: "libomero_client.so" as "target/lib/libomero_client.so" >>>> scons: *** [target/lib/libomero_client.so] libomero_client.so: No such file or directory >>> >>> Can you try setting the following: >>> >>> export CPPPATH=/usr/include >>> export CXX=g++ >>> export VERBOSE=1 >> >> The problem here is most likely using the default system compiler, which >> chokes on the broken Ice headers. This is what causes the Ice/Ice.h not >> found error (the diagnostic here is poor--the header does exist, but the >> test for it fails because the header is not valid C++, and newer GCC >> versions have stricter C++ syntax checking). If you look with the >> verbose logging, you'll probably see that g++ errors out. >> >> If you install g++-4.4 and try building with >> CXX=g++-4.4 >> you might have a little more success. Not ideal, but Ice is broken and >> that's currently the only option. >> >> >> Regards, >> Roger From m.woodbridge at imperial.ac.uk Mon Feb 18 10:03:03 2013 From: m.woodbridge at imperial.ac.uk (Mark Woodbridge) Date: Mon, 18 Feb 2013 10:03:03 +0000 Subject: [ome-users] OMERO 4.4.6 and Python 2.4 Message-ID: <5121FC57.3020905@imperial.ac.uk> Hi, I've just attempted an upgrade of OMERO from 4.4.4 to 4.4.6. It no longer seems to work on Python 2.4 (use of try-except-finally in lib/python/omero/plugins/admin.py). This is a problem because 2.4 is the Python version in RHEL 5, which we're not quite ready to abandon! Mark. From r.leigh at dundee.ac.uk Mon Feb 18 10:08:03 2013 From: r.leigh at dundee.ac.uk (Roger Leigh) Date: Mon, 18 Feb 2013 10:08:03 +0000 Subject: [ome-users] Bio-Formats ImageJ bit depth In-Reply-To: References: Message-ID: <5121FD83.5060402@dundee.ac.uk> On 16/02/2013 16:24, Tom Bongiorno wrote: > Hello, I am using the Bio-Formats plugin on ImageJ to import JPEG2000 > images. Although all the images are 16-bit, when using the "Measure" > command, the dynamic range of the mean pixel value seems to be variable > (i.e. dependent on the particular image). If I select part of my image > and run the "Fill" command (to get a black square), the mean pixel value > will be 0. But when I run the "Invert" command on the filled region (to > get a white square), the mean pixel value is inconsistent (I'd expect > 65535). Some values I've gotten are 1757, 2449, 6832, and 7902. > > Any assistance or explanation would be greatly appreciated. Hi Tom, This looks like it's down to the way imagej implements the "invert" command--it's not specific to the Bio-Formats plugin. The invert command inverts within the range of the min/max pixel intensity of all the pixels of your image, rather than the full 16-bit range. In all your examples above, the range of values you get are probably the value of the max intensity pixel in your image. See invert16BitStack() in ij/plugin/filter/Filters.java. I agree that this is not entirely intuitive! Select all, set min/max grey level in analyze->set measurements, and then analyze->measure to determine that, for example. If what you want is a complete inversion of the full 16-bit range, I suggest as a workaround that you create an image of the same size and bit depth with all pixels set to 65535, and then use the calculator/calculator plus to subtract your image from this one, which should do what you want. Regards, Roger -- Dr Roger Leigh -- Open Microscopy Environment Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH Scotland UK Tel: (01382) 386364 The University of Dundee is a registered Scottish Charity, No: SC015096 From bernd.jagla at pasteur.fr Mon Feb 18 12:52:52 2013 From: bernd.jagla at pasteur.fr (Bernd Jagla) Date: Mon, 18 Feb 2013 13:52:52 +0100 Subject: [ome-users] Installation feedback Message-ID: <51222424.4060606@pasteur.fr> Installation problems: Rather a protocol of what I am doing... 1. After downloading the server I cannot find any installer/documentation inside the zip file... (I then found a link on the download page to a well written installation page) 2. https://www.openmicroscopy.org/site/support/omero4/sysadmins/windows/server-installation.html: - I am using Windows 7... It is not listed. I would like to see a table with the supported OSs... (that would give me confidence that someone was successful with this...) - a short explanation why the 32 bit version of Python is needed and not the 64-bit would help me to be more confident in what I am doing right now... - you write: "May already have been installed as a dependency of Matplot Lib." : how do I check this? - I am having problems compiling/installing NumPy, hopeing it is already installed... - with regards to pytables: I found http://www.lfd.uci.edu/~gohlke/pythonlibs/#pytables to be working the easiest.. (now also installing numpy-MKL, scipy, ndimage, tables) - should I install the 32bit version of postgresDB? I believe not... going for 64Bit... - First, go to/File ? Options/select the/Browser/tab a should include "Display" (i.e. I believe the screen shots are different... I am using 1.16.1 of pgAdmin) - diagnostics: ================================================================================ OMERO Diagnostics 4.4.6-ice34-b102 ================================================================================ Commands: java -version 1.7.0 (C:\Windows\system32\java.EXE) Commands: python -V 2.6.6 (C:\Python26\python.EXE -- 2 others) Commands: icegridnode --version 3.4.2 (C:\Ice\Ice-3.4.2\bin\icegridnode.EXE) Commands: icegridadmin --version 3.4.2 (C:\Ice\Ice-3.4.2\bin\icegridadmin.EXE) Commands: psql --version not found Server: icegridnode not started Cannot list deployed applications. Log dir: C:\omero.server\var\log exists Log files: Blitz-0.log n/a Log files: DropBox.log n/a Log files: FileServer.log n/a Log files: Indexer-0.log n/a Log files: MonitorServer.log n/a Log files: OMEROweb.log n/a Log files: Processor-0.log n/a Log files: Tables-0.log n/a Log files: TestDropBox.log n/a Log files: Total size 0.00 MB Error while parsing logs Environment:OMERO_HOME=(unset) Environment:OMERO_NODE=(unset) Environment:OMERO_MASTER=(unset) Environment:PATH=C:\Ice\Ice-3.4.2\bin;C:\Python26;C:\Program Files\ImageMagick-6.8.2-Q16;C:\Program Files (x86)\AMD APP\bin\x86_64;C:\Program Files (x86)\AMD APP\bin\x86; C:\Program Files (x86)\Intel\iCLS Client\;C:\Program Files\Intel\iCLS Client\;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShel l\v1.0\;C:\Program Files\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files\Intel\Intel(R) Management Engine Components\IPT;C:\Program Files (x86)\Intel\Int el(R) Management Engine Components\DAL;C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\IPT;C:\Program Files (x86)\ATI Technologies\ATI.ACE\Core-Static; c:\cygwin\bin;C:\Program Files\TortoiseSVN\bin;C:\Program Files\TortoiseGit\bin;C:\Program Files (x86)\CVSNT\;c:\ant\bin Environment:ICE_HOME=(unset) Environment:LD_LIBRARY_PATH=(unset) Environment:DYLD_LIBRARY_PATH=(unset) OMERO data dir: '/OMERO' Exists? True Is writable? True OMERO.web status... [NOT STARTED] ============================================ -- I conclude that psql is not on the PATH... adding it... -- "Server: icegridnode not started" ??? never saw icegridnode before in the docs... --- searched for it on the installation web page... nothing... ---- searching FAQ : nothing... --- searching documentation ... nothing... => I am stuck... I'll keep trying, but usually it is about now that I will do something stupid... Be aware ;) -------------- next part -------------- An HTML attachment was scrubbed... URL: From b.pindelski at dundee.ac.uk Mon Feb 18 13:28:36 2013 From: b.pindelski at dundee.ac.uk (Blazej Pindelski) Date: Mon, 18 Feb 2013 13:28:36 +0000 Subject: [ome-users] OMERO 4.4.6 and Python 2.4 In-Reply-To: <5121FC57.3020905@imperial.ac.uk> References: <5121FC57.3020905@imperial.ac.uk> Message-ID: Hi Mark, Thanks for pin-pointing this error. Please accept my apologies for letting it slip the QA radar. The corrected version of admin.py can be downloaded from https://raw.github.com/bpindelski/openmicroscopy/58729dbcfad50b6b7f540d4c1a13f2e79ae5fd2e/components/tools/OmeroPy/src/omero/plugins/admin.py. This will allow you to proceed with the upgrade. I've also opened a ticket (https://trac.openmicroscopy.org.uk/ome/ticket/10412), which I've CC'd you on and a pull request (https://github.com/openmicroscopy/openmicroscopy/pull/757) to fix the issue. It will be merged into the codebase in the next bug-fix release of OMERO. Regards, -- Blazej Pindelski Software Developer Open Microscopy Environment http://www.openmicroscopy.org On 18 Feb 2013, at 10:03, Mark Woodbridge wrote: > Hi, > > I've just attempted an upgrade of OMERO from 4.4.4 to 4.4.6. It no longer seems to work on Python 2.4 (use of try-except-finally in lib/python/omero/plugins/admin.py). This is a problem because 2.4 is the Python version in RHEL 5, which we're not quite ready to abandon! > > Mark. > _______________________________________________ > ome-users mailing list > ome-users at lists.openmicroscopy.org.uk > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users > The University of Dundee is a registered Scottish Charity, No: SC015096 From m.woodbridge at imperial.ac.uk Mon Feb 18 13:40:05 2013 From: m.woodbridge at imperial.ac.uk (Mark Woodbridge) Date: Mon, 18 Feb 2013 13:40:05 +0000 Subject: [ome-users] OMERO 4.4.6 and Python 2.4 In-Reply-To: References: <5121FC57.3020905@imperial.ac.uk> Message-ID: <51222F35.2000007@imperial.ac.uk> Hi Blazej, Many thanks for the quick fix. I commented out the offending lines, which allowed me to make the config changes that we needed and complete the upgrade anyway. But now I have replaced it with your corrected version and it works fine. Thanks again, Mark. On 18/02/13 13:28, Blazej Pindelski wrote: > Hi Mark, > > Thanks for pin-pointing this error. Please accept my apologies for letting it slip the QA radar. The corrected version of admin.py can be downloaded from https://raw.github.com/bpindelski/openmicroscopy/58729dbcfad50b6b7f540d4c1a13f2e79ae5fd2e/components/tools/OmeroPy/src/omero/plugins/admin.py. > This will allow you to proceed with the upgrade. > > I've also opened a ticket (https://trac.openmicroscopy.org.uk/ome/ticket/10412), which I've CC'd you on and a pull request (https://github.com/openmicroscopy/openmicroscopy/pull/757) to fix the issue. > It will be merged into the codebase in the next bug-fix release of OMERO. > > Regards, > -- > Blazej Pindelski > Software Developer > Open Microscopy Environment > http://www.openmicroscopy.org > > On 18 Feb 2013, at 10:03, Mark Woodbridge wrote: > >> Hi, >> >> I've just attempted an upgrade of OMERO from 4.4.4 to 4.4.6. It no longer seems to work on Python 2.4 (use of try-except-finally in lib/python/omero/plugins/admin.py). This is a problem because 2.4 is the Python version in RHEL 5, which we're not quite ready to abandon! >> >> Mark. >> _______________________________________________ >> ome-users mailing list >> ome-users at lists.openmicroscopy.org.uk >> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users >> > > > The University of Dundee is a registered Scottish Charity, No: SC015096 > From josh at glencoesoftware.com Mon Feb 18 13:55:02 2013 From: josh at glencoesoftware.com (Josh Moore) Date: Mon, 18 Feb 2013 14:55:02 +0100 Subject: [ome-users] Installation feedback In-Reply-To: <51222424.4060606@pasteur.fr> References: <51222424.4060606@pasteur.fr> Message-ID: <4FCBAC85-FCDA-4701-AE83-92DAB816CDF0@glencoesoftware.com> Hi Bernd, On Feb 18, 2013, at 1:52 PM, Bernd Jagla wrote: > Installation problems: > > Rather a protocol of what I am doing... > > > 1. After downloading the server I cannot find any installer/documentation inside the zip file... > (I then found a link on the download page to a well written installation page) > 2. https://www.openmicroscopy.org/site/support/omero4/sysadmins/windows/server-installation.html: > - I am using Windows 7... It is not listed. I would like to see a table with the supported OSs... (that would give me confidence that someone was successful with this...) > - a short explanation why the 32 bit version of Python is needed and not the 64-bit would help me to be more confident in what I am doing right now... > - you write: "May already have been installed as a dependency of Matplot Lib." : how do I check this? > - I am having problems compiling/installing NumPy, hopeing it is already installed... > - with regards to pytables: I found http://www.lfd.uci.edu/~gohlke/pythonlibs/#pytables to be working the easiest.. > (now also installing numpy-MKL, scipy, ndimage, tables) > - should I install the 32bit version of postgresDB? I believe not... going for 64Bit... > - First, go to/File ? Options/select the/Browser/tab a should include "Display" (i.e. I believe the screen shots are different... I am using 1.16.1 of pgAdmin) > - diagnostics: > ================================================================================ > OMERO Diagnostics 4.4.6-ice34-b102 > ================================================================================ > > Commands: java -version 1.7.0 (C:\Windows\system32\java.EXE) > Commands: python -V 2.6.6 (C:\Python26\python.EXE -- 2 others) > Commands: icegridnode --version 3.4.2 (C:\Ice\Ice-3.4.2\bin\icegridnode.EXE) > Commands: icegridadmin --version 3.4.2 (C:\Ice\Ice-3.4.2\bin\icegridadmin.EXE) > Commands: psql --version not found > > Server: icegridnode not started > > Cannot list deployed applications. > > Log dir: C:\omero.server\var\log exists > > Log files: Blitz-0.log n/a > Log files: DropBox.log n/a > Log files: FileServer.log n/a > Log files: Indexer-0.log n/a > Log files: MonitorServer.log n/a > Log files: OMEROweb.log n/a > Log files: Processor-0.log n/a > Log files: Tables-0.log n/a > Log files: TestDropBox.log n/a > Log files: Total size 0.00 MB > > Error while parsing logs > > Environment:OMERO_HOME=(unset) > Environment:OMERO_NODE=(unset) > Environment:OMERO_MASTER=(unset) > Environment:PATH=C:\Ice\Ice-3.4.2\bin;C:\Python26;C:\Program Files\ImageMagick-6.8.2-Q16;C:\Program Files (x86)\AMD APP\bin\x86_64;C:\Program Files (x86)\AMD APP\bin\x86; > C:\Program Files (x86)\Intel\iCLS Client\;C:\Program Files\Intel\iCLS Client\;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShel > l\v1.0\;C:\Program Files\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files\Intel\Intel(R) Management Engine Components\IPT;C:\Program Files (x86)\Intel\Int > el(R) Management Engine Components\DAL;C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\IPT;C:\Program Files (x86)\ATI Technologies\ATI.ACE\Core-Static; > c:\cygwin\bin;C:\Program Files\TortoiseSVN\bin;C:\Program Files\TortoiseGit\bin;C:\Program Files (x86)\CVSNT\;c:\ant\bin > Environment:ICE_HOME=(unset) > Environment:LD_LIBRARY_PATH=(unset) > Environment:DYLD_LIBRARY_PATH=(unset) > > OMERO data dir: '/OMERO' Exists? True Is writable? True > OMERO.web status... [NOT STARTED] > ============================================ > > -- I conclude that psql is not on the PATH... adding it... > > -- "Server: icegridnode not started" > ??? never saw icegridnode before in the docs... > --- searched for it on the installation web page... nothing... > ---- searching FAQ : nothing... > --- searching documentation ... nothing... > > => I am stuck... > > I'll keep trying, but usually it is about now that I will do something stupid... > > Be aware ;) Then we had better respond quickly! Much of the above will have to be processed into documentation additions/changes, but our initial thanks for all the feedback. As for getting your server started, what was the output of running `bin\omero admin start`? And because this is the part that I always forget under Windows, did you open the console "Run as administrator..."? If there are any new files under var\log after trying to run from an admin console (assuming things don't work), please send those along. Best wishes, ~Josh From m.spitaler at imperial.ac.uk Tue Feb 19 12:07:20 2013 From: m.spitaler at imperial.ac.uk (Martin Spitaler) Date: Tue, 19 Feb 2013 12:07:20 +0000 Subject: [ome-users] searching bug In-Reply-To: References: Message-ID: <51236AF8.60901@imperial.ac.uk> Dear Omero developers, we have just installed the new version, but I was very disappointed to see that searching still doesn't work, when I search for a tag linked to 228 images I still get 7 results, and for other search none at all. I know this has been reported before by several users, but the latest entry on the respective ticket (https://trac.openmicroscopy.org.uk/ome/ticket/9385) is five months old and says "changed from OMERO-4.4.4 to OMERO-4.5" - is anything being done about it, and what is the plan for it to be solved? For us, this really is a major impediment for people to use Omero, because quite obviously if you upload lots of data and can't find them, it's defying all the other fancy things we can now do with Omero (and there are quite a few of them now, thanks). Best, Martin -- ------------------------------------------------------------------------ *Martin Spitaler, PhD* *FILM - Facility for Imaging by Light Microscopy* - Facility Manager - Sir Alexander Fleming Building, desk 401 Imperial College London / South Kensington Exhibition Road London SW7 2AZ UK Tel. +44-(0)20-759-42023 E-mail m.spitaler at imperial.ac.uk Website: http://imperial.ac.uk/imagingfacility -------------- next part -------------- An HTML attachment was scrubbed... URL: From callan at glencoesoftware.com Tue Feb 19 14:05:42 2013 From: callan at glencoesoftware.com (Chris Allan) Date: Tue, 19 Feb 2013 14:05:42 +0000 Subject: [ome-users] OME-XML File In-Reply-To: References: Message-ID: <5B2A5FBD-A736-401D-89B6-E7A637FB267B@glencoesoftware.com> Hi Leandro, Your best bet for working with this is the OMEXMLFactory in the Bio-Formats OME-XML component: https://github.com/openmicroscopy/bioformats/blob/develop/components/ome-xml/src/ome/xml/OMEXMLFactory.java You can then modify the resulting OME-XML model object hierarchy and then write it out as XML in memory or to a stream. -Chris On 17 Feb 2013, at 23:28, Leandro Bugnon wrote: > Dear developers, > > I need to write a file with metadata only (OME-XML) for configuration purposes. What class could I use to do this?. IFileWriter asks me an image, but i only need the metadata. > > Thank you very much. > > Best Regards, > > -- > Leandro > _______________________________________________ > ome-users mailing list > ome-users at lists.openmicroscopy.org.uk > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users From ctrueden at wisc.edu Tue Feb 19 19:39:25 2013 From: ctrueden at wisc.edu (Curtis Rueden) Date: Tue, 19 Feb 2013 13:39:25 -0600 Subject: [ome-users] [Software Feedback] LOCI plugin bug In-Reply-To: References: Message-ID: Hi Daniel, > When you export a time series let's assume with 5 time points, the > first time point is exported correctly, but then the following ones > have an issue. Please update your Fiji to the latest version (Help > Update Fiji) and try again. If the problem still occurs, let us know. In that case though, we may need a test file or macro; you can upload one using the Help > Upload Sample Image command if needed. Regards, Curtis On Tue, Feb 12, 2013 at 10:14 AM, wrote: > Dear all, I have been using your LOCI plugin to export some ics/ids > time-series stacks using FIJI. I have noticed there is a bug on this > feature. When you export a time series let's assume with 5 time points, the > first time point is exported correctly, but then the following ones have an > issue. For example time-point 3 instead of being exported as a single > frame, is exported as an ics stack with 3 frames, 2 empty frames and the > last one is the actual single frame you would want to be exported to begin > with. In summary, each time-point is exported as a stack with a number of > frames equal to the time point number. This bug only seems to occur for ics > files. If you could help me and look into this it would be greatly > appreciated. > > All the best, > > Daniel Martins > -------------- next part -------------- An HTML attachment was scrubbed... URL: From P.Thomas at uea.ac.uk Wed Feb 20 08:28:49 2013 From: P.Thomas at uea.ac.uk (Paul Thomas (BIO)) Date: Wed, 20 Feb 2013 08:28:49 +0000 Subject: [ome-users] [Software Feedback] LOCI plugin bug In-Reply-To: References: Message-ID: <813C5441A8B6B5439711C30EB6A9EB5004A20A@ueastfexch01.UEA.AC.UK> I too have a problem with the ics export; although, I thought that it was a problem with the files I am using. I import an ome.tif using LOCI and then export to ics. My problem is that I want a single ics file from a time series, not individual files for each time point. If in the dialogue box I choose NOT to "write each...to a separate file", I get an exception: java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at ij.Command.runPlugIn(Command.java:148) at ij.Command.runCommand(Command.java:97) at ij.Executer.run(Executer.java:64) at java.lang.Thread.run(Thread.java:619) Caused by: java.lang.IllegalArgumentException: Invalid Z size: 0 at loci.formats.FormatTools.getZCTCoords(FormatTools.java:403) at loci.plugins.out.Exporter.run(Exporter.java:545) at loci.plugins.LociExporter.run(LociExporter.java:77) at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:262) at ij.plugin.filter.PlugInFilterRunner.(PlugInFilterRunner.java:111) at ij.IJ.runUserPlugIn(IJ.java:187) at ij.IJ.runPlugIn(IJ.java:152) ... 8 more However, if I choose to export to separate files, it works. Also, if I choose to export the channels and Zs (i.e., frames are NOT present) to separate files and leave the timepoints unchecked it also works. ____________________ Dr. Paul Thomas, Director, The Henry Wellcome Laboratory for Cell Imaging, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom. e-mail: p.thomas at uea.ac.uk Tel: +44-1603-592196 Fax: +44-1603-592250 Imaging web-site: http://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab Personal web-page: http://biobis.bio.uea.ac.uk/biosql/fac_show.aspx?ID=548 From: ome-users-bounces at lists.openmicroscopy.org.uk [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Curtis Rueden Sent: 19 February 2013 19:39 To: daniel.martins at oncology.ox.ac.uk Cc: OME-users mailing list Subject: Re: [ome-users] [Software Feedback] LOCI plugin bug Hi Daniel, > When you export a time series let's assume with 5 time points, the > first time point is exported correctly, but then the following ones > have an issue. Please update your Fiji to the latest version (Help > Update Fiji) and try again. If the problem still occurs, let us know. In that case though, we may need a test file or macro; you can upload one using the Help > Upload Sample Image command if needed. Regards, Curtis On Tue, Feb 12, 2013 at 10:14 AM, > wrote: Dear all, I have been using your LOCI plugin to export some ics/ids time-series stacks using FIJI. I have noticed there is a bug on this feature. When you export a time series let's assume with 5 time points, the first time point is exported correctly, but then the following ones have an issue. For example time-point 3 instead of being exported as a single frame, is exported as an ics stack with 3 frames, 2 empty frames and the last one is the actual single frame you would want to be exported to begin with. In summary, each time-point is exported as a stack with a number of frames equal to the time point number. This bug only seems to occur for ics files. If you could help me and look into this it would be greatly appreciated. All the best, Daniel Martins -------------- next part -------------- An HTML attachment was scrubbed... URL: From P.Thomas at uea.ac.uk Wed Feb 20 09:19:57 2013 From: P.Thomas at uea.ac.uk (Paul Thomas (BIO)) Date: Wed, 20 Feb 2013 09:19:57 +0000 Subject: [ome-users] [Software Feedback] LOCI plugin bug In-Reply-To: References: Message-ID: <813C5441A8B6B5439711C30EB6A9EB5004A261@ueastfexch01.UEA.AC.UK> I've now tried to open an ics file generated by LOCI using the SLIM plugin (Lifetime) and got the same exceptions. (All with the most up-to-date version of Fiji.) Paul ____________________ Dr. Paul Thomas, Director, The Henry Wellcome Laboratory for Cell Imaging, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom. e-mail: p.thomas at uea.ac.uk Tel: +44-1603-592196 Fax: +44-1603-592250 Imaging web-site: http://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab Personal web-page: http://biobis.bio.uea.ac.uk/biosql/fac_show.aspx?ID=548 From: ome-users-bounces at lists.openmicroscopy.org.uk [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Curtis Rueden Sent: 19 February 2013 19:39 To: daniel.martins at oncology.ox.ac.uk Cc: OME-users mailing list Subject: Re: [ome-users] [Software Feedback] LOCI plugin bug Hi Daniel, > When you export a time series let's assume with 5 time points, the > first time point is exported correctly, but then the following ones > have an issue. Please update your Fiji to the latest version (Help > Update Fiji) and try again. If the problem still occurs, let us know. In that case though, we may need a test file or macro; you can upload one using the Help > Upload Sample Image command if needed. Regards, Curtis On Tue, Feb 12, 2013 at 10:14 AM, > wrote: Dear all, I have been using your LOCI plugin to export some ics/ids time-series stacks using FIJI. I have noticed there is a bug on this feature. When you export a time series let's assume with 5 time points, the first time point is exported correctly, but then the following ones have an issue. For example time-point 3 instead of being exported as a single frame, is exported as an ics stack with 3 frames, 2 empty frames and the last one is the actual single frame you would want to be exported to begin with. In summary, each time-point is exported as a stack with a number of frames equal to the time point number. This bug only seems to occur for ics files. If you could help me and look into this it would be greatly appreciated. All the best, Daniel Martins -------------- next part -------------- An HTML attachment was scrubbed... URL: From will at lifesci.dundee.ac.uk Wed Feb 20 10:00:13 2013 From: will at lifesci.dundee.ac.uk (Will Moore) Date: Wed, 20 Feb 2013 10:00:13 +0000 Subject: [ome-users] searching bug In-Reply-To: <51236AF8.60901@imperial.ac.uk> References: <51236AF8.60901@imperial.ac.uk> Message-ID: <024059E4-1F0D-4D5A-8F2E-3DBAAD64B635@lifesci.dundee.ac.uk> Hi Martin, Thanks for your feedback. The OMERO team will discuss this in some more detail soon - but at the moment we can't tell you when we're going to focus specifically on search. Part of the problem with search is that we've never had a good test set of data and expected search results, so testing has been a bit haphazard. However, we have now started to prepare a test set of data so we can run some search tests and clarify the issues. Then we'll have a clearer idea of what's needed to fix the problems you're seeing. We are also planning to align the search UI in Insight and Web clients, so if you have any feedback on missing or important search features, that would be great to hear. If you have specific requirements beyond basic image name / description search, let us know so we can include this in our tests (and if you have sample data, that's always useful too). Many thanks, Will. On 19 Feb 2013, at 12:07, Martin Spitaler wrote: > Dear Omero developers, > > we have just installed the new version, but I was very disappointed to see that searching still doesn't work, when I search for a tag linked to 228 images I still get 7 results, and for other search none at all. > > I know this has been reported before by several users, but the latest entry on the respective ticket (https://trac.openmicroscopy.org.uk/ome/ticket/9385) is five months old and says "changed from OMERO-4.4.4 to OMERO-4.5" - is anything being done about it, and what is the plan for it to be solved? > > For us, this really is a major impediment for people to use Omero, because quite obviously if you upload lots of data and can't find them, it's defying all the other fancy things we can now do with Omero (and there are quite a few of them now, thanks). > > Best, > > Martin > > -- > Martin Spitaler, PhD > FILM - Facility for Imaging by Light Microscopy > - Facility Manager - > Sir Alexander Fleming Building, desk 401 > Imperial College London / South Kensington > Exhibition Road > London SW7 2AZ > UK > > Tel. +44-(0)20-759-42023 > E-mail m.spitaler at imperial.ac.uk > Website: http://imperial.ac.uk/imagingfacility > > _______________________________________________ > ome-users mailing list > ome-users at lists.openmicroscopy.org.uk > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.spitaler at imperial.ac.uk Wed Feb 20 10:48:16 2013 From: m.spitaler at imperial.ac.uk (Martin Spitaler) Date: Wed, 20 Feb 2013 10:48:16 +0000 Subject: [ome-users] searching bug In-Reply-To: <024059E4-1F0D-4D5A-8F2E-3DBAAD64B635@lifesci.dundee.ac.uk> References: <51236AF8.60901@imperial.ac.uk> <024059E4-1F0D-4D5A-8F2E-3DBAAD64B635@lifesci.dundee.ac.uk> Message-ID: <5124A9F0.9010109@imperial.ac.uk> Thanks, Will. Ideas for missing search features: First, some traditional functions: * IMAGE TYPE, e.g. time series, stack, multi-channel...; maybe even specifying a specific range (number of channels or time points) * METADATA SEARCH, e.g. a specific microscope, lens or excitation laser; would also help with the above (e.g. search for "confocal images with the 2 channels GFP+DAPI" * ADVANCED SEARCH, i.e. the user can search for different things in different fields, PUBMED-style And then an idea that came from one of our users, saying the typical situation is having an image and wanting to find related ones, but not remembering how to search for them (I seem to remember this has already been discussed at OME meetings): * SIMILAR IMAGES: some of this functionality would be covered by METADATA and IMAGE TYPE search above, but an additional feature that sounds doable is mean and standard deviation of intensities I know this last idea opens a whole new world of complexity, and also workload for servers if calculated automatically (although once done, it would only be two more numbers per frame to store), but maybe one or a few of the scripting aficionados could help with this? Would it be possible to run a script on a dataset calculating such values and adding them to the metadata? Long-term, the ideal situation would be to have a tick box on data import to do this calculation if wanted, and a script to do it later if not ticked on import. Obviously there is no limit to ideas, in an ideal world (now still dream land), analysis results could be linked to images and allow searches like "images with >100 cells" or "cells with 'roundness>1.5'. And in a world where photographic cameras take pictures when people smile, it's not inconceivable to have basic analysis like counting nuclei on import. But that's something after version 4.5 (and 5) - maybe someone in the community wants to have a play? Good work, Martin -- ------------------------------------------------------------------------ *Martin Spitaler, PhD* *FILM - Facility for Imaging by Light Microscopy* - Facility Manager - Sir Alexander Fleming Building, desk 401 Imperial College London / South Kensington Exhibition Road London SW7 2AZ UK Tel. +44-(0)20-759-42023 E-mail m.spitaler at imperial.ac.uk Website: http://imperial.ac.uk/imagingfacility -------------- next part -------------- An HTML attachment was scrubbed... URL: From melissa at glencoesoftware.com Wed Feb 20 21:00:33 2013 From: melissa at glencoesoftware.com (Melissa Linkert) Date: Wed, 20 Feb 2013 16:00:33 -0500 Subject: [ome-users] [Software Feedback] LOCI plugin bug In-Reply-To: <813C5441A8B6B5439711C30EB6A9EB5004A20A@ueastfexch01.UEA.AC.UK> References: <813C5441A8B6B5439711C30EB6A9EB5004A20A@ueastfexch01.UEA.AC.UK> Message-ID: <20130220210033.GB2196@medusa> Hi Paul, > I too have a problem with the ics export; although, I thought that it was a problem with the files I am using. I import an ome.tif using LOCI and then export to ics. My problem is that I want a single ics file from a time series, not individual files for each time point. If in the dialogue box I choose NOT to "write each...to a separate file", I get an exception: > > java.lang.reflect.InvocationTargetException > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) > at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) > at java.lang.reflect.Method.invoke(Method.java:597) > at ij.Command.runPlugIn(Command.java:148) > at ij.Command.runCommand(Command.java:97) > at ij.Executer.run(Executer.java:64) > at java.lang.Thread.run(Thread.java:619) > Caused by: java.lang.IllegalArgumentException: Invalid Z size: 0 > at loci.formats.FormatTools.getZCTCoords(FormatTools.java:403) > at loci.plugins.out.Exporter.run(Exporter.java:545) > at loci.plugins.LociExporter.run(LociExporter.java:77) > at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:262) > at ij.plugin.filter.PlugInFilterRunner.(PlugInFilterRunner.java:111) > at ij.IJ.runUserPlugIn(IJ.java:187) > at ij.IJ.runPlugIn(IJ.java:152) > ... 8 more > > However, if I choose to export to separate files, it works. Also, if I choose to export the channels and Zs (i.e., frames are NOT present) to separate files and leave the timepoints unchecked it also works. Running "Help > Update Fiji" should solve this problem, but do note that there is an outstanding bug in the ICS writer which affects some multi-channel datasets. We are testing a fix for that now, and should have it resolved shortly. Regards, -Melissa On Wed, Feb 20, 2013 at 08:28:49AM +0000, Paul Thomas (BIO) wrote: > I too have a problem with the ics export; although, I thought that it was a problem with the files I am using. I import an ome.tif using LOCI and then export to ics. My problem is that I want a single ics file from a time series, not individual files for each time point. If in the dialogue box I choose NOT to "write each...to a separate file", I get an exception: > > java.lang.reflect.InvocationTargetException > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) > at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) > at java.lang.reflect.Method.invoke(Method.java:597) > at ij.Command.runPlugIn(Command.java:148) > at ij.Command.runCommand(Command.java:97) > at ij.Executer.run(Executer.java:64) > at java.lang.Thread.run(Thread.java:619) > Caused by: java.lang.IllegalArgumentException: Invalid Z size: 0 > at loci.formats.FormatTools.getZCTCoords(FormatTools.java:403) > at loci.plugins.out.Exporter.run(Exporter.java:545) > at loci.plugins.LociExporter.run(LociExporter.java:77) > at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:262) > at ij.plugin.filter.PlugInFilterRunner.(PlugInFilterRunner.java:111) > at ij.IJ.runUserPlugIn(IJ.java:187) > at ij.IJ.runPlugIn(IJ.java:152) > ... 8 more > > However, if I choose to export to separate files, it works. Also, if I choose to export the channels and Zs (i.e., frames are NOT present) to separate files and leave the timepoints unchecked it also works. > > ____________________ > Dr. Paul Thomas, Director, > The Henry Wellcome Laboratory for Cell Imaging, > School of Biological Sciences, > University of East Anglia, > Norwich Research Park, > Norwich, > NR4 7TJ, > United Kingdom. > > e-mail: p.thomas at uea.ac.uk > Tel: +44-1603-592196 > Fax: +44-1603-592250 > Imaging web-site: http://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab > Personal web-page: http://biobis.bio.uea.ac.uk/biosql/fac_show.aspx?ID=548 > > From: ome-users-bounces at lists.openmicroscopy.org.uk [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Curtis Rueden > Sent: 19 February 2013 19:39 > To: daniel.martins at oncology.ox.ac.uk > Cc: OME-users mailing list > Subject: Re: [ome-users] [Software Feedback] LOCI plugin bug > > Hi Daniel, > > > When you export a time series let's assume with 5 time points, the > > first time point is exported correctly, but then the following ones > > have an issue. > > Please update your Fiji to the latest version (Help > Update Fiji) and try again. If the problem still occurs, let us know. In that case though, we may need a test file or macro; you can upload one using the Help > Upload Sample Image command if needed. > > Regards, > Curtis > > > On Tue, Feb 12, 2013 at 10:14 AM, > wrote: > Dear all, I have been using your LOCI plugin to export some ics/ids time-series stacks using FIJI. I have noticed there is a bug on this feature. When you export a time series let's assume with 5 time points, the first time point is exported correctly, but then the following ones have an issue. For example time-point 3 instead of being exported as a single frame, is exported as an ics stack with 3 frames, 2 empty frames and the last one is the actual single frame you would want to be exported to begin with. In summary, each time-point is exported as a stack with a number of frames equal to the time point number. This bug only seems to occur for ics files. If you could help me and look into this it would be greatly appreciated. > > All the best, > > Daniel Martins > > _______________________________________________ > ome-users mailing list > ome-users at lists.openmicroscopy.org.uk > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users From melissa at glencoesoftware.com Wed Feb 20 21:02:31 2013 From: melissa at glencoesoftware.com (Melissa Linkert) Date: Wed, 20 Feb 2013 16:02:31 -0500 Subject: [ome-users] [Software Feedback] LOCI plugin bug In-Reply-To: <813C5441A8B6B5439711C30EB6A9EB5004A261@ueastfexch01.UEA.AC.UK> References: <813C5441A8B6B5439711C30EB6A9EB5004A261@ueastfexch01.UEA.AC.UK> Message-ID: <20130220210231.GC2196@medusa> Hi Paul, > I've now tried to open an ics file generated by LOCI using the SLIM plugin (Lifetime) and got the same exceptions. (All with the most up-to-date version of Fiji.) The error message sent previously would only occur when writing an ICS file. Could you please double-check that your Fiji is completely up to date, and then send the complete error message that you see when reading the ICS file created by the SLIM plugin? Regards, -Melissa On Wed, Feb 20, 2013 at 09:19:57AM +0000, Paul Thomas (BIO) wrote: > I've now tried to open an ics file generated by LOCI using the SLIM plugin (Lifetime) and got the same exceptions. (All with the most up-to-date version of Fiji.) > Paul > > ____________________ > Dr. Paul Thomas, Director, > The Henry Wellcome Laboratory for Cell Imaging, > School of Biological Sciences, > University of East Anglia, > Norwich Research Park, > Norwich, > NR4 7TJ, > United Kingdom. > > e-mail: p.thomas at uea.ac.uk > Tel: +44-1603-592196 > Fax: +44-1603-592250 > Imaging web-site: http://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab > Personal web-page: http://biobis.bio.uea.ac.uk/biosql/fac_show.aspx?ID=548 > > From: ome-users-bounces at lists.openmicroscopy.org.uk [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Curtis Rueden > Sent: 19 February 2013 19:39 > To: daniel.martins at oncology.ox.ac.uk > Cc: OME-users mailing list > Subject: Re: [ome-users] [Software Feedback] LOCI plugin bug > > Hi Daniel, > > > When you export a time series let's assume with 5 time points, the > > first time point is exported correctly, but then the following ones > > have an issue. > > Please update your Fiji to the latest version (Help > Update Fiji) and try again. If the problem still occurs, let us know. In that case though, we may need a test file or macro; you can upload one using the Help > Upload Sample Image command if needed. > > Regards, > Curtis > > > On Tue, Feb 12, 2013 at 10:14 AM, > wrote: > Dear all, I have been using your LOCI plugin to export some ics/ids time-series stacks using FIJI. I have noticed there is a bug on this feature. When you export a time series let's assume with 5 time points, the first time point is exported correctly, but then the following ones have an issue. For example time-point 3 instead of being exported as a single frame, is exported as an ics stack with 3 frames, 2 empty frames and the last one is the actual single frame you would want to be exported to begin with. In summary, each time-point is exported as a stack with a number of frames equal to the time point number. This bug only seems to occur for ics files. If you could help me and look into this it would be greatly appreciated. > > All the best, > > Daniel Martins > > _______________________________________________ > ome-users mailing list > ome-users at lists.openmicroscopy.org.uk > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users From will at lifesci.dundee.ac.uk Wed Feb 20 23:37:20 2013 From: will at lifesci.dundee.ac.uk (Will Moore) Date: Wed, 20 Feb 2013 23:37:20 +0000 Subject: [ome-users] searching bug In-Reply-To: <5124A9F0.9010109@imperial.ac.uk> References: <51236AF8.60901@imperial.ac.uk> <024059E4-1F0D-4D5A-8F2E-3DBAAD64B635@lifesci.dundee.ac.uk> <5124A9F0.9010109@imperial.ac.uk> Message-ID: <9663CC90-A6C6-4568-9A75-0A95D17D352F@lifesci.dundee.ac.uk> Hi Martin, I thought I'd try to explore the "Metadata Search" you described below, so I've written a script that takes a few search parameters, builds a database query and then tags the resulting images. Script is here https://github.com/will-moore/scripts/blob/metadata_search/omero/search_scripts/Metadata_Search.py See screenshots below for the script search form and the results. You can search for any combination of search fields. When the script has finished, refresh your Tags view and you'll see a "Search Results " Tag with the resulting images. NB: In the right panel you'll notice that the description of the Tag has a summary of what you searched for. Have a play with it and let us know what you think (E.g. what other search fields do we need?). Once we have something we're happy with, we can implement it in the clients "properly". Cheers, Will. On 20 Feb 2013, at 10:48, Martin Spitaler wrote: > Thanks, Will. > > Ideas for missing search features: First, some traditional functions: > IMAGE TYPE, e.g. time series, stack, multi-channel...; maybe even specifying a specific range (number of channels or time points) > METADATA SEARCH, e.g. a specific microscope, lens or excitation laser; would also help with the above (e.g. search for "confocal images with the 2 channels GFP+DAPI" > ADVANCED SEARCH, i.e. the user can search for different things in different fields, PUBMED-style > And then an idea that came from one of our users, saying the typical situation is having an image and wanting to find related ones, but not remembering how to search for them (I seem to remember this has already been discussed at OME meetings): > SIMILAR IMAGES: some of this functionality would be covered by METADATA and IMAGE TYPE search above, but an additional feature that sounds doable is mean and standard deviation of intensities > I know this last idea opens a whole new world of complexity, and also workload for servers if calculated automatically (although once done, it would only be two more numbers per frame to store), but maybe one or a few of the scripting aficionados could help with this? Would it be possible to run a script on a dataset calculating such values and adding them to the metadata? Long-term, the ideal situation would be to have a tick box on data import to do this calculation if wanted, and a script to do it later if not ticked on import. > > Obviously there is no limit to ideas, in an ideal world (now still dream land), analysis results could be linked to images and allow searches like "images with >100 cells" or "cells with 'roundness>1.5'. And in a world where photographic cameras take pictures when people smile, it's not inconceivable to have basic analysis like counting nuclei on import. But that's something after version 4.5 (and 5) - maybe someone in the community wants to have a play? > > Good work, > > Martin > -- > Martin Spitaler, PhD > FILM - Facility for Imaging by Light Microscopy > - Facility Manager - > Sir Alexander Fleming Building, desk 401 > Imperial College London / South Kensington > Exhibition Road > London SW7 2AZ > UK > > Tel. +44-(0)20-759-42023 > E-mail m.spitaler at imperial.ac.uk > Website: http://imperial.ac.uk/imagingfacility > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen shot 2013-02-20 at 23.24.01.png Type: image/png Size: 77123 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen shot 2013-02-20 at 23.31.00.png Type: image/png Size: 160814 bytes Desc: not available URL: From bembenek at utk.edu Thu Feb 21 19:01:32 2013 From: bembenek at utk.edu (Joshua Bembenek) Date: Thu, 21 Feb 2013 14:01:32 -0500 Subject: [ome-users] Quicktime Export Options Message-ID: Hello, I switched to using Fiji, but I cannot find the quicktime export functionality. Previously I was able to select several options for quicktime export. Also, BioFormats does not allow any options for making quicktime movies. Am I missing something? Josh -- Joshua N. Bembenek, PhD Assistant Professor UT Knoxville, BCMB 1414 Cumberland Ave C211 Walter Life Sciences Building Knoxville, TN 37996 Office: (865) 974-4085 Lab: (865) 974-3815 From melissa at glencoesoftware.com Thu Feb 21 19:15:28 2013 From: melissa at glencoesoftware.com (Melissa Linkert) Date: Thu, 21 Feb 2013 14:15:28 -0500 Subject: [ome-users] Quicktime Export Options In-Reply-To: References: Message-ID: <20130221191528.GC2285@medusa> Hi Josh, > I switched to using Fiji, but I cannot find the quicktime export > functionality. Previously I was able to select several options for > quicktime export. I can't speak to that really, but it's possible that whichever plugin you were using previously is not included in Fiji. > Also, BioFormats does not allow any options for > making quicktime movies. Am I missing something? "Plugins > LOCI > Bio-Formats Exporter" should allow you to save uncompressed movies - just make sure to set the file name extension to ".mov". Regards, -Melissa On Thu, Feb 21, 2013 at 02:01:32PM -0500, Joshua Bembenek wrote: > Hello, > > I switched to using Fiji, but I cannot find the quicktime export > functionality. Previously I was able to select several options for > quicktime export. Also, BioFormats does not allow any options for > making quicktime movies. Am I missing something? > > Josh > > -- > Joshua N. Bembenek, PhD > Assistant Professor > UT Knoxville, BCMB > 1414 Cumberland Ave > C211 Walter Life Sciences Building > Knoxville, TN 37996 > Office: (865) 974-4085 > Lab: (865) 974-3815 > _______________________________________________ > ome-users mailing list > ome-users at lists.openmicroscopy.org.uk > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users From melissa at glencoesoftware.com Fri Feb 22 18:04:33 2013 From: melissa at glencoesoftware.com (Melissa Linkert) Date: Fri, 22 Feb 2013 13:04:33 -0500 Subject: [ome-users] ZeissZVIReader help In-Reply-To: <999BD541C12A2D4D878D79277024D8B347FDE3F7@exmbx13.ex.ad3.ucdavis.edu> References: <999BD541C12A2D4D878D79277024D8B347FDE3F7@exmbx13.ex.ad3.ucdavis.edu> Message-ID: <20130222180433.GD2318@medusa> Hi Peter, (CC'ing the ome-users mailing list, as that is the best place to ask Bio-Formats questions.) > I am a .NET programmer at UC Davis. I have a client with 3000+ zvi images with associated metadata in the author, comment and keywords fields. I am looking for a method to process these files and extract the zvi image and thumbnail and display them, as well as extracting the needed metadata. > > I am not familiar with java, but I can learn. IKVM.NET provides a framework that enables Java and .NET interoperability (http://www.ikvm.net). > > I'm wondering if you could share any code that does this or provide me any references. If you haven't already, I would suggest reading this section of the Bio-Formats documentation: https://www.openmicroscopy.org/site/support/bio-formats/developers/non-java-code.html I don't have any direct experience with IKVM, unfortunately, but hopefully that gives you a place to start. Regards, -Melissa On Fri, Feb 22, 2013 at 05:33:17AM +0000, Peter J Hunter wrote: > Melissa, > I am a .NET programmer at UC Davis. I have a client with 3000+ zvi images with associated metadata in the author, comment and keywords fields. I am looking for a method to process these files and extract the zvi image and thumbnail and display them, as well as extracting the needed metadata. > > I am not familiar with java, but I can learn. IKVM.NET provides a framework that enables Java and .NET interoperability (http://www.ikvm.net). > > I'm wondering if you could share any code that does this or provide me any references. > Thanks! > > Peter J. Hunter > From ctrueden at wisc.edu Fri Feb 22 19:18:54 2013 From: ctrueden at wisc.edu (Curtis Rueden) Date: Fri, 22 Feb 2013 13:18:54 -0600 Subject: [ome-users] ZeissZVIReader help In-Reply-To: <20130222180433.GD2318@medusa> References: <999BD541C12A2D4D878D79277024D8B347FDE3F7@exmbx13.ex.ad3.ucdavis.edu> <20130222180433.GD2318@medusa> Message-ID: Hi Peter, I briefly investigated using Bio-Formats with IKVM.NET in 2007, but concluded that it was too slow for our needs at the time. Even then though, it ostensibly worked, which is pretty impressive for a project of that scope. And of course, six years later now, I have heard that IKVM.NET is much improved. You would obviously have to try for yourself, but I am guessing for your needs it might be a good match. As for learning Java, fortunately, C# and Java are extremely similar languages. So hopefully you will not find it too difficult to study the code examples and adapt them for use in your .NET application. If you get something working, we would love to hear back about it! We could post more specific information about .NET & Bio-Formats to the web site for the benefit of others, if you have any tips, pitfalls, etc., that you want to share. Thanks, Curtis On Fri, Feb 22, 2013 at 12:04 PM, Melissa Linkert < melissa at glencoesoftware.com> wrote: > Hi Peter, > > (CC'ing the ome-users mailing list, as that is the best place to ask > Bio-Formats questions.) > > > I am a .NET programmer at UC Davis. I have a client with 3000+ zvi > images with associated metadata in the author, comment and keywords fields. > I am looking for a method to process these files and extract the zvi image > and thumbnail and display them, as well as extracting the needed metadata. > > > > I am not familiar with java, but I can learn. IKVM.NET provides a > framework that enables Java and .NET interoperability (http://www.ikvm.net > ). > > > > I'm wondering if you could share any code that does this or provide me > any references. > > If you haven't already, I would suggest reading this section of the > Bio-Formats documentation: > > > https://www.openmicroscopy.org/site/support/bio-formats/developers/non-java-code.html > > I don't have any direct experience with IKVM, unfortunately, but > hopefully that gives you a place to start. > > Regards, > -Melissa > > On Fri, Feb 22, 2013 at 05:33:17AM +0000, Peter J Hunter wrote: > > Melissa, > > I am a .NET programmer at UC Davis. I have a client with 3000+ zvi > images with associated metadata in the author, comment and keywords fields. > I am looking for a method to process these files and extract the zvi image > and thumbnail and display them, as well as extracting the needed metadata. > > > > I am not familiar with java, but I can learn. IKVM.NET provides a > framework that enables Java and .NET interoperability (http://www.ikvm.net > ). > > > > I'm wondering if you could share any code that does this or provide me > any references. > > Thanks! > > > > Peter J. Hunter > > > _______________________________________________ > ome-users mailing list > ome-users at lists.openmicroscopy.org.uk > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dsudar at lbl.gov Sat Feb 23 01:16:03 2013 From: dsudar at lbl.gov (Damir Sudar) Date: Fri, 22 Feb 2013 17:16:03 -0800 Subject: [ome-users] slow or failing import of large files with large X by Y size Message-ID: <51281853.1090601@lbl.gov> Hi all, On my installation (Omero 4.4.5/Ice 3.4 on Ubuntu 12.04LTS 64-bit) I see the following strange import (using Insight/Importer 4.4.5) behavior: File1.lsm: 102MB is 5120 by 5120 pixels in 2 channels takes 30-40 minutes to import File2.lsm: 207MB is 1024 by 1024 pixels by 50 Z-slices takes 1 minute to import File3.tif: 100MB is 10240 by 10240 pixels simple 8-bit TIFF, import finishes in a few seconds without errors but the resulting image in Omero will not open and gives error: "The image could not be opened. The image is not a valid image." But the archived version can be downloaded without trouble. So there appears to be something wrong with importing image with large X by Y sizes. Has anyone seen this as well and is there a solution? Thanks, - Damir -- Damir Sudar - Staff Scientist and Deputy for Technology Lawrence Berkeley Laboratory / Life Sciences Division One Cyclotron Road, MS 977, Berkeley, CA 94720, USA T: 510/486-5346 - F: 510/486-5586 - E: DSudar at lbl.gov WWW: http://www.lbl.gov/lsd/People_&_Organization/Scientific_Staff_Directory/Sudar_Lab.html From melissa at glencoesoftware.com Sat Feb 23 19:22:45 2013 From: melissa at glencoesoftware.com (Melissa Linkert) Date: Sat, 23 Feb 2013 14:22:45 -0500 Subject: [ome-users] [locisoftware] Opening ND2 files (Nikon) with ImageJ via Bio-Formats In-Reply-To: <51268541.06c7640a.2a92.ffffb97bSMTPIN_ADDED_MISSING@mx.google.com> References: <51268541.06c7640a.2a92.ffffb97bSMTPIN_ADDED_MISSING@mx.google.com> Message-ID: <20130223192245.GA2230@medusa> Hi Chris, (CC'ing the ome-users mailing list; that is the best place to ask Bio-Formats questions.) > I am getting inconsistent results with my ND2 files. > Sometimes they open via BIO-formats, and sometimes they don't. > > I updated to the latest ImageJ (1.47k) and bioformats > (02/21/2013), but my "broken" files still will not open. > The error is attached below. Thank you for the bug report; unfortunately, we don't yet have any files that produce this error. Would you be willing to send one of the problematic files? If so, you can upload files here: http://qa.openmicroscopy.org.uk/qa/upload/ If that doesn't work, please let me know and I will send alternate upload instructions. Regards, -Melissa On Thu, Feb 21, 2013 at 02:34:40PM -0600, chris richie wrote: > I am getting inconsistent results with my ND2 files. > Sometimes they open via BIO-formats, and sometimes they don't. > > I updated to the latest ImageJ (1.47k) and bioformats > (02/21/2013), but my "broken" files still will not open. > The error is attached below. > > any ideas? > > Thanks > chris > > > > java.lang.StackOverflowError > at java.nio.ByteOrder.nativeOrder(Unknown Source) > at java.nio.DirectByteBuffer.get(Unknown Source) > at java.nio.HeapByteBuffer.put(Unknown Source) > at sun.nio.ch.IOUtil.read(Unknown Source) > at sun.nio.ch.FileChannelImpl.read(Unknown Source) > at ome.scifio.io.NIOFileHandle.read(NIOFileHandle.java:245) > at ome.scifio.io.NIOFileHandle.read(NIOFileHandle.java:232) > at ome.scifio.io.RandomAccessInputStream.read(RandomAccessInputStream.java:441) > at sun.nio.cs.StreamDecoder.readBytes(Unknown Source) > at sun.nio.cs.StreamDecoder.implRead(Unknown Source) > at sun.nio.cs.StreamDecoder.read(Unknown Source) > at java.io.InputStreamReader.read(Unknown Source) > at ome.scifio.io.RandomAccessInputStream.findString(RandomAccessInputStream.java:308) > at ome.scifio.io.RandomAccessInputStream.findString(RandomAccessInputStream.java:217) > at ome.scifio.io.RandomAccessInputStream.readCString(RandomAccessInputStream.java:387) > at loci.common.RandomAccessInputStream.readCString(RandomAccessInputStream.java:269) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1500) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at 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loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1537) > > From melissa at glencoesoftware.com Sat Feb 23 19:32:59 2013 From: melissa at glencoesoftware.com (Melissa Linkert) Date: Sat, 23 Feb 2013 14:32:59 -0500 Subject: [ome-users] Quicktime Export Options In-Reply-To: References: <20130221191528.GC2285@medusa> Message-ID: <20130223193259.GB2230@medusa> Hi Josh, > Thanks for the fast response. Previously I could select compression > formats, and also frame rate of the movie. I don't see these options > with the BioFormats. Is my only option using an older imageJ with the > old quicktime exporter plugins? Bio-Formats only supports writing compressed Quicktime movies if QuickTime for Java is installed; if it isn't installed, then you won't see a prompt for the compression type. The movie's frame rate will correspond to whatever is in the "Frame interval" field when you select "Image > Properties", so you can certainly change it but Bio-Formats' exporter plugin won't prompt for it separately. Regards, -Melissa On Thu, Feb 21, 2013 at 02:55:29PM -0500, Joshua Bembenek wrote: > Melissa, > > Thanks for the fast response. Previously I could select compression > formats, and also frame rate of the movie. I don't see these options > with the BioFormats. Is my only option using an older imageJ with the > old quicktime exporter plugins? > > Thanks, > > Josh > > On Thu, Feb 21, 2013 at 2:15 PM, Melissa Linkert > wrote: > > Hi Josh, > > > >> I switched to using Fiji, but I cannot find the quicktime export > >> functionality. Previously I was able to select several options for > >> quicktime export. > > > > I can't speak to that really, but it's possible that whichever plugin > > you were using previously is not included in Fiji. > > > >> Also, BioFormats does not allow any options for > >> making quicktime movies. Am I missing something? > > > > "Plugins > LOCI > Bio-Formats Exporter" should allow you to save > > uncompressed movies - just make sure to set the file name extension to > > ".mov". > > > > Regards, > > -Melissa > > > > On Thu, Feb 21, 2013 at 02:01:32PM -0500, Joshua Bembenek wrote: > >> Hello, > >> > >> I switched to using Fiji, but I cannot find the quicktime export > >> functionality. Previously I was able to select several options for > >> quicktime export. Also, BioFormats does not allow any options for > >> making quicktime movies. Am I missing something? > >> > >> Josh > >> > >> -- > >> Joshua N. Bembenek, PhD > >> Assistant Professor > >> UT Knoxville, BCMB > >> 1414 Cumberland Ave > >> C211 Walter Life Sciences Building > >> Knoxville, TN 37996 > >> Office: (865) 974-4085 > >> Lab: (865) 974-3815 > >> _______________________________________________ > >> ome-users mailing list > >> ome-users at lists.openmicroscopy.org.uk > >> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users > > > > > > -- > Joshua N. Bembenek, PhD > Assistant Professor > UT Knoxville, BCMB > 1414 Cumberland Ave > C211 Walter Life Sciences Building > Knoxville, TN 37996 > Office: (865) 974-4085 > Lab: (865) 974-3815 From p.walczysko at dundee.ac.uk Mon Feb 25 09:50:32 2013 From: p.walczysko at dundee.ac.uk (Petr Walczysko) Date: Mon, 25 Feb 2013 09:50:32 +0000 Subject: [ome-users] slow or failing import of large files with large X by Y size In-Reply-To: <51281853.1090601@lbl.gov> References: <51281853.1090601@lbl.gov> Message-ID: <62886BD2-24CB-48DF-A013-736C9C5506A2@dundee.ac.uk> Hello Damir Thank you very much for your feedback. Could you please upload the files in question using out QA ? Please go to http://qa.openmicroscopy.org.uk/qa/upload/ and follow the instructions. It would help us to investigate the problem. Thank you All the best Petr On 23 Feb 2013, at 01:16, Damir Sudar > wrote: Hi all, On my installation (Omero 4.4.5/Ice 3.4 on Ubuntu 12.04LTS 64-bit) I see the following strange import (using Insight/Importer 4.4.5) behavior: File1.lsm: 102MB is 5120 by 5120 pixels in 2 channels takes 30-40 minutes to import File2.lsm: 207MB is 1024 by 1024 pixels by 50 Z-slices takes 1 minute to import File3.tif: 100MB is 10240 by 10240 pixels simple 8-bit TIFF, import finishes in a few seconds without errors but the resulting image in Omero will not open and gives error: "The image could not be opened. The image is not a valid image." But the archived version can be downloaded without trouble. So there appears to be something wrong with importing image with large X by Y sizes. Has anyone seen this as well and is there a solution? Thanks, - Damir -- Damir Sudar - Staff Scientist and Deputy for Technology Lawrence Berkeley Laboratory / Life Sciences Division One Cyclotron Road, MS 977, Berkeley, CA 94720, USA T: 510/486-5346 - F: 510/486-5586 - E: DSudar at lbl.gov WWW: http://www.lbl.gov/lsd/People_&_Organization/Scientific_Staff_Directory/Sudar_Lab.html _______________________________________________ ome-users mailing list ome-users at lists.openmicroscopy.org.uk http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users The University of Dundee is a registered Scottish Charity, No: SC015096 -------------- next part -------------- An HTML attachment was scrubbed... URL: From keng.hng at csc.mrc.ac.uk Mon Feb 25 16:02:54 2013 From: keng.hng at csc.mrc.ac.uk (Hng, Keng) Date: Mon, 25 Feb 2013 16:02:54 +0000 Subject: [ome-users] Metadata error Message-ID: <4A1CB892B9A4894DA2DE77F2FE2C514930A5B276@icexch-m5.ic.ac.uk> Hello, I had been using FiJi with Loci revion cef7286 build 8 December 2011, Release 4.4-DEV on Image 1.46A to extract and rename 10+gb sized .lif files. These were massive 10x10x100 tile scans which we stitch using FiJi. Upon updating ImageJ to 1.47K and Loci to revision 093faed built February 2013, Release 4.5-DEV, bioformats no longer extracted the metadata for Tile|Pos Y (any number higher than 0) These were the values I was using for renaming the extracted tif files for each tile of the large tile scans. At the moment I'm regressing and using an older version of FiJi, but if the meta data could be added back into the newer version, that will be much appreciated. Thank you very much for your help. Ki Keng Imm Hng Microscopy Facility MRC Clinical Sciences Centre Faculty of Medicine, Imperial College London Hammersmith Hospital Campus Du Cane Road London W12 0NN Tel: 020 8383 8528 Email: keng.hng at csc.mrc.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From dsudar at lbl.gov Mon Feb 25 20:24:40 2013 From: dsudar at lbl.gov (Damir Sudar) Date: Mon, 25 Feb 2013 12:24:40 -0800 Subject: [ome-users] slow or failing import of large files with large X by Y size In-Reply-To: <62886BD2-24CB-48DF-A013-736C9C5506A2@dundee.ac.uk> References: <51281853.1090601@lbl.gov> <62886BD2-24CB-48DF-A013-736C9C5506A2@dundee.ac.uk> Message-ID: <512BC888.7090902@lbl.gov> Hi Petr, Thanks for the quick response. I've just uploaded the 3 files described below. I'm mostly concerned at this point about the import failure of file3.tif. Thanks, - Damir On 2/25/2013 1:50 AM, Petr Walczysko wrote: > Hello Damir > > Thank you very much for your feedback. > Could you please upload the files in question using out QA ? > Please go to > http://qa.openmicroscopy.org.uk/qa/upload/ > and follow the instructions. > It would help us to investigate the problem. > Thank you > All the best > Petr > > > > On 23 Feb 2013, at 01:16, Damir Sudar > > wrote: > >> Hi all, >> >> On my installation (Omero 4.4.5/Ice 3.4 on Ubuntu 12.04LTS 64-bit) I >> see the following strange import (using Insight/Importer 4.4.5) behavior: >> File1.lsm: 102MB is 5120 by 5120 pixels in 2 channels takes 30-40 >> minutes to import >> File2.lsm: 207MB is 1024 by 1024 pixels by 50 Z-slices takes 1 >> minute to import >> File3.tif: 100MB is 10240 by 10240 pixels simple 8-bit TIFF, import >> finishes in a few seconds without errors but the resulting image in >> Omero will not open and gives error: "The image could not be opened. >> The image is not a valid image." But the archived version can be >> downloaded without trouble. >> >> So there appears to be something wrong with importing image with >> large X by Y sizes. Has anyone seen this as well and is there a solution? >> >> Thanks, >> - Damir >> >> -- >> Damir Sudar - Staff Scientist and Deputy for Technology >> Lawrence Berkeley Laboratory / Life Sciences Division >> One Cyclotron Road, MS 977, Berkeley, CA 94720, USA >> T: 510/486-5346 - F: 510/486-5586 - E: DSudar at lbl.gov >> >> WWW: >> http://www.lbl.gov/lsd/People_&_Organization/Scientific_Staff_Directory/Sudar_Lab.html >> >> _______________________________________________ >> ome-users mailing list >> ome-users at lists.openmicroscopy.org.uk >> >> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users >> > > > The University of Dundee is a registered Scottish Charity, No: SC015096 -- Damir Sudar - Staff Scientist and Deputy for Technology Lawrence Berkeley Laboratory / Life Sciences Division One Cyclotron Road, MS 977, Berkeley, CA 94720, USA T: 510/486-5346 - F: 510/486-5586 - E: DSudar at lbl.gov WWW: http://www.lbl.gov/lsd/People_&_Organization/Scientific_Staff_Directory/Sudar_Lab.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.leigh at dundee.ac.uk Tue Feb 26 09:39:25 2013 From: r.leigh at dundee.ac.uk (Roger Leigh) Date: Tue, 26 Feb 2013 09:39:25 +0000 Subject: [ome-users] Metadata error In-Reply-To: <4A1CB892B9A4894DA2DE77F2FE2C514930A5B276@icexch-m5.ic.ac.uk> References: <4A1CB892B9A4894DA2DE77F2FE2C514930A5B276@icexch-m5.ic.ac.uk> Message-ID: <512C82CD.4070805@dundee.ac.uk> On 25/02/13 16:02, Hng, Keng wrote: > Upon updating ImageJ to 1.47K and Loci to revision 093faed built > February 2013, Release 4.5-DEV, bioformats no longer extracted the > metadata for Tile|Pos Y (any number higher than 0) These were the values > I was using for renaming the extracted tif files for each tile of the > large tile scans. At the moment I?m regressing and using an older > version of FiJi, but if the meta data could be added back into the newer > version, that will be much appreciated. Could you possibly upload one of these files so that we could take a look in more detail? You can do this here: http://qa.openmicroscopy.org.uk/qa/upload/ The smallest of your files which demonstrates the problem should be sufficient. Many thanks, Roger Leigh -- Dr Roger Leigh -- Open Microscopy Environment Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH Scotland UK Tel: (01382) 386364 The University of Dundee is a registered Scottish Charity, No: SC015096 From melissa at glencoesoftware.com Wed Feb 27 07:31:39 2013 From: melissa at glencoesoftware.com (Melissa Linkert) Date: Wed, 27 Feb 2013 02:31:39 -0500 Subject: [ome-users] slow or failing import of large files with large X by Y size In-Reply-To: <512BC888.7090902@lbl.gov> References: <51281853.1090601@lbl.gov> <62886BD2-24CB-48DF-A013-736C9C5506A2@dundee.ac.uk> <512BC888.7090902@lbl.gov> Message-ID: <20130227073139.GA12856@medusa> Hi Damir, > Thanks for the quick response. I've just uploaded the 3 files > described below. I'm mostly concerned at this point about the import > failure of file3.tif. Thank you for uploading the problematic files. It looks like there are two distinct problems: one is that file3.tif is not viewable (which I can reproduce), and the other is the time required to import .lsm files (which I cannot reproduce). For the file3.tif problem, increasing the amount of memory available to the server should help. It looks like that file was saved using ImageJ; for the future, you may wish to use the Bio-Formats exporter plugin to save TIFFs from ImageJ, as that will save TIFFs in such a way as to prevent this problem without requiring more memory. For the .lsm import times, I consistently see that file1.lsm imports in 10-12 minutes (also on Ubuntu 12.04 with Ice 3.4). Are you able to consistently reproduce that that file takes 30+ minutes? If so, could you please send a copy of the server logs so that we can investigate further? Regards, -Melissa On Mon, Feb 25, 2013 at 12:24:40PM -0800, Damir Sudar wrote: > Hi Petr, > > Thanks for the quick response. I've just uploaded the 3 files > described below. I'm mostly concerned at this point about the import > failure of file3.tif. > > Thanks, > - Damir > On 2/25/2013 1:50 AM, Petr Walczysko wrote: > >Hello Damir > > > >Thank you very much for your feedback. > >Could you please upload the files in question using out QA ? > >Please go to > >http://qa.openmicroscopy.org.uk/qa/upload/ > >and follow the instructions. > >It would help us to investigate the problem. > >Thank you > >All the best > >Petr > > > > > > > >On 23 Feb 2013, at 01:16, Damir Sudar >> > > wrote: > > > >>Hi all, > >> > >>On my installation (Omero 4.4.5/Ice 3.4 on Ubuntu 12.04LTS > >>64-bit) I see the following strange import (using > >>Insight/Importer 4.4.5) behavior: > >>File1.lsm: 102MB is 5120 by 5120 pixels in 2 channels takes > >>30-40 minutes to import > >>File2.lsm: 207MB is 1024 by 1024 pixels by 50 Z-slices takes 1 > >>minute to import > >>File3.tif: 100MB is 10240 by 10240 pixels simple 8-bit TIFF, > >>import finishes in a few seconds without errors but the > >>resulting image in Omero will not open and gives error: "The > >>image could not be opened. The image is not a valid image." But > >>the archived version can be downloaded without trouble. > >> > >>So there appears to be something wrong with importing image with > >>large X by Y sizes. Has anyone seen this as well and is there a > >>solution? > >> > >>Thanks, > >>- Damir > >> > >>-- > >>Damir Sudar - Staff Scientist and Deputy for Technology > >>Lawrence Berkeley Laboratory / Life Sciences Division > >>One Cyclotron Road, MS 977, Berkeley, CA 94720, USA > >>T: 510/486-5346 - F: 510/486-5586 - E: DSudar at lbl.gov > >> > >>WWW: http://www.lbl.gov/lsd/People_&_Organization/Scientific_Staff_Directory/Sudar_Lab.html > >> > >>_______________________________________________ > >>ome-users mailing list > >>ome-users at lists.openmicroscopy.org.uk > >> > >>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users > >> > > > > > >The University of Dundee is a registered Scottish Charity, No: > >SC015096 > > -- > Damir Sudar - Staff Scientist and Deputy for Technology > Lawrence Berkeley Laboratory / Life Sciences Division > One Cyclotron Road, MS 977, Berkeley, CA 94720, USA > T: 510/486-5346 - F: 510/486-5586 - E: DSudar at lbl.gov > WWW: http://www.lbl.gov/lsd/People_&_Organization/Scientific_Staff_Directory/Sudar_Lab.html > > _______________________________________________ > ome-users mailing list > ome-users at lists.openmicroscopy.org.uk > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users From pierre.pouchin at udamail.fr Thu Feb 28 12:56:37 2013 From: pierre.pouchin at udamail.fr (Pierre Pouchin) Date: Thu, 28 Feb 2013 13:56:37 +0100 Subject: [ome-users] Dropbox : "Bad session key" Message-ID: <512F5405.2030401@udamail.fr> Hi, This morning, a user tried to import a hundred tif on OMERO through the dropbox system, but after 70 imports, it stopped. In the log file, I can see that 10 minutes and 8 seconds after it started importing the files, a "bad session key" error shows up each time it tries to import an image. What can I change to prevent this behavior ? Regards, Pierre From volker.hilsenstein at embl.de Thu Feb 28 13:45:25 2013 From: volker.hilsenstein at embl.de (Volker Hilsenstein) Date: Thu, 28 Feb 2013 14:45:25 +0100 Subject: [ome-users] ScanR file conversion to OME Tiff - feature request In-Reply-To: References: Message-ID: Dear OME users/developers, I have a feature request regarding the handling of ScanR data, in particular when doing a batch conversion to OME tiff. First off, I have to admit that I'm only superficially familiar with bioformats/LOCI but I have inherited some legacy code from a software engineer that now works elsewhere. First off, a short problem description: we are a microscopy facility and we use the ScanR microscopes for many of the high-throughput screens run by our users and visitors. We use a legacy script that calls bioformats for converting the ScanR tiff files to OME tiff with an OME tiff filename convention. For this script the software engineer forked an earlier version of bioformats and made some modifications. >From my understanding the main modification added by our software engineer was to address the following issue: Apparently, the ScanR output contains a list of all the filenames of the run as Metadata. For a large well plate with many subpositions this can be several thousands of file names, which are often very long due to deeply nested paths. When running a batch conversion this Metadata gets added to the header of each individual tiff image, which can increase the size of each image by several megabytes. He also added some other changes, but I am fairly confident these could be added outside of the main bioformats code. >From our point of view, it would be convenient if the possibility of stripping the list of filenames from the metadata was added as an option to the main branch of bioformats. Is this something you'd be willing to consider? Kind regards, Volker -------------- next part -------------- An HTML attachment was scrubbed... URL: From C.Blackburn at dundee.ac.uk Thu Feb 28 17:03:11 2013 From: C.Blackburn at dundee.ac.uk (Colin Blackburn) Date: Thu, 28 Feb 2013 17:03:11 +0000 Subject: [ome-users] Dropbox : "Bad session key" In-Reply-To: <512F5405.2030401@udamail.fr> References: <512F5405.2030401@udamail.fr> Message-ID: <1F632E94-CC20-4271-A56E-C311A511EDB7@dundee.ac.uk> Hi Pierre, Could you let me know the operating system your server is running, your OMERO server version and the typical tif file size, assuming they were all similar sizes? Did the user copy the files into just one directory? Can you send the zipped up log files that cover the failure directly to me if possible? Cheers, Colin On 28 Feb 2013, at 12:56, Pierre Pouchin wrote: > Hi, > > > This morning, a user tried to import a hundred tif on OMERO through the dropbox system, but after 70 imports, it stopped. > In the log file, I can see that 10 minutes and 8 seconds after it started importing the files, a "bad session key" error shows up each time it tries to import an image. > > What can I change to prevent this behavior ? > > > Regards, > > Pierre > _______________________________________________ > ome-users mailing list > ome-users at lists.openmicroscopy.org.uk > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users > The University of Dundee is a registered Scottish Charity, No: SC015096