<div dir="ltr">Hi Roger-<div><br></div><div>Thanks so much. I thought I had updated Fiji, but I may have one that only after testing for IDS/ICS, and after I updated, I may have only tested OME.TIF. I will test this tonight. </div><div><br></div><div>I would indeed like to be added to the ticket for whether BigTIFF will be automatically enabled for OME.TIF when using the bioformats exporter. Can you add my e-mail to this ticket? <a href="mailto:scientistmiller@gmail.com">scientistmiller@gmail.com</a>.</div><div><br></div><div>Thanks so very much for your help.</div><div>-Jason<br><div class="gmail_extra"><br><div class="gmail_quote">On Fri, May 1, 2015 at 7:00 AM, <span dir="ltr"><<a href="mailto:ome-users-request@lists.openmicroscopy.org.uk" target="_blank">ome-users-request@lists.openmicroscopy.org.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send ome-users mailing list submissions to<br>
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Today's Topics:<br>
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1. Re: Saving large files in ome.tif or ids/ics (Roger Leigh)<br>
2. One week left to register for the Paris Users Meeting!<br>
(Helen Flynn (Staff))<br>
3. OMERO Scripts Plugins (Stephen Taylor)<br>
4. Re: OMERO Scripts Plugins (William Moore)<br>
5. Re: OMERO Scripts Plugins (Stephen Taylor)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Fri, 1 May 2015 08:50:49 +0000<br>
From: Roger Leigh <<a href="mailto:r.leigh@dundee.ac.uk">r.leigh@dundee.ac.uk</a>><br>
To: <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>><br>
Subject: Re: [ome-users] Saving large files in ome.tif or ids/ics<br>
Message-ID: <<a href="mailto:55433E69.5060100@dundee.ac.uk">55433E69.5060100@dundee.ac.uk</a>><br>
Content-Type: text/plain; charset="windows-1252"; format=flowed<br>
<br>
On 30/04/2015 21:40, Jason Miller wrote:<br>
<br>
Dear Jason,<br>
<br>
> Similar to recent past posts on this list, I'm having trouble saving<br>
> files that are > 4GB into ome.tif or IDS/ICS formats. I have a 5GB file,<br>
> open as a virtual file, and when I go to export via Bioformats Exporter<br>
> to IDS/ICS format, I get the following error:<br>
[stacktrace]<br>
<br>
For IDS/ICS, this was fixed in this PR last week:<br>
<a href="https://github.com/openmicroscopy/bioformats/pull/1738" target="_blank">https://github.com/openmicroscopy/bioformats/pull/1738</a><br>
I have tested this with >5GB images and it works correctly.<br>
<br>
> When I go to export to ome.tif format, I get the same error previously<br>
> reported on this list:<br>
> loci.formats.FormatException: File is too large; call setBigTiff(true)<br>
><br>
> Is it possible to retain the ome.tif format for >4GB? In my case, this<br>
> is for importing into Huygens for deconvolution.<br>
<br>
For plain (not OME) TIFF:<br>
<a href="https://github.com/openmicroscopy/bioformats/pull/1744" target="_blank">https://github.com/openmicroscopy/bioformats/pull/1744</a><br>
<br>
Both of the above fixes are in the newly-released Bio-Formats 5.1.1<br>
release. If using Fiji, you should automatically get this update; for<br>
ImageJ you can download the updated plugin from<br>
<a href="http://downloads.openmicroscopy.org/bio-formats/5.1.1/" target="_blank">http://downloads.openmicroscopy.org/bio-formats/5.1.1/</a><br>
<br>
For OME-TIFF, it's not currently possible to enable BigTIFF when<br>
exporting from ImageJ using the exporter dialogue. For the plain TIFF<br>
case, rather than relying on an API call to enable BigTIFF, we now<br>
enable it if the image data is >4GiB or a "big" TIFF file extension such<br>
as .btf, .tf8 or .tf2 is used. We would like to do the same for<br>
OME-TIFF, but this first requires updating the OME-TIFF specification<br>
which currently only allows a .ome.tiff or .ome.tif file extension.<br>
Once that's done, you would be able to use e.g. ".ome.btf" and get a<br>
"big" OME-TIFF file. However, this does require some consideration<br>
since (for example) these files would not be readable with older<br>
versions of Bio-Formats unless you renamed them to ".ome.tiff" after export.<br>
<br>
To summarise, it isn't currently possible to export >4GB ome.tiff files<br>
using the Bio-Formats Exporter. It is possible via the Java API by<br>
calling writer.setBigTiff(true) if this is an option for you. This is a<br>
known limitation which we are working on; see the discussion in the PR<br>
#1744 above.<br>
<br>
There is a ticket open here for this:<br>
<a href="https://trac.openmicroscopy.org/ome/ticket/12858" target="_blank">https://trac.openmicroscopy.org/ome/ticket/12858</a><br>
I can add you as a CC on it if you like, so you'll be kept up to date<br>
with its progress?<br>
<br>
<br>
Kind regards,<br>
Roger<br>
<br>
--<br>
Dr Roger Leigh -- Open Microscopy Environment<br>
Wellcome Trust Centre for Gene Regulation and Expression,<br>
College of Life Sciences, University of Dundee, Dow Street,<br>
Dundee DD1 5EH Scotland UK Tel: (01382) 386364<br>
<br>
The University of Dundee is a registered Scottish Charity, No: SC015096<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Fri, 1 May 2015 08:56:58 +0000<br>
From: "Helen Flynn (Staff)" <<a href="mailto:h.flynn@dundee.ac.uk">h.flynn@dundee.ac.uk</a>><br>
To: "<<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>>"<br>
<<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>>,<br>
"<<a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a>>"<br>
<<a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a>><br>
Subject: [ome-users] One week left to register for the Paris Users<br>
Meeting!<br>
Message-ID: <<a href="mailto:DDCB0DD8-60C6-4A22-B65C-C34B1C6DBC62@dundee.ac.uk">DDCB0DD8-60C6-4A22-B65C-C34B1C6DBC62@dundee.ac.uk</a>><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
Dear All,<br>
<br>
Just to remind you, if you are planning to come to the Paris Users Meeting June 2nd & 3rd, you have one week left to book your place.<br>
<br>
The programme is up at <a href="https://www.openmicroscopy.org/site/community/minutes/meetings/10th-annual-users-meeting-june-2015" target="_blank">https://www.openmicroscopy.org/site/community/minutes/meetings/10th-annual-users-meeting-june-2015</a><br>
and you can book via<br>
<a href="http://www.buyat.dundee.ac.uk/browse/extra_info.asp?compid=1&modid=2&catid=62&prodid=437" target="_blank">http://www.buyat.dundee.ac.uk/browse/extra_info.asp?compid=1&modid=2&catid=62&prodid=437</a><br>
<br>
This is a great opportunity to find out what other people are doing with OMERO & Bio-Formats and to discuss what you want out of our software with our developers. We hope to see you there!<br>
<br>
Regards,<br>
<br>
The OME Team<br>
<br>
Dr Helen Flynn<br>
OME Technical Writer<br>
Centre for Gene Regulation & Expression<br>
Open Microscopy Environment<br>
University of Dundee<br>
<a href="http://openmicroscopy.org" target="_blank">http://openmicroscopy.org</a><<a href="http://openmicroscopy.org/" target="_blank">http://openmicroscopy.org/</a>><br>
<br>
<br>
The University of Dundee is a registered Scottish Charity, No: SC015096<br>
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Message: 3<br>
Date: Fri, 1 May 2015 09:04:01 +0000<br>
From: Stephen Taylor <<a href="mailto:stephen.taylor@imm.ox.ac.uk">stephen.taylor@imm.ox.ac.uk</a>><br>
To: "<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>"<br>
<<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>><br>
Subject: [ome-users] OMERO Scripts Plugins<br>
Message-ID:<br>
<<a href="mailto:2574ACA6D1653848AAAE2E439508A9064710D2@MBX06.ad.oak.ox.ac.uk">2574ACA6D1653848AAAE2E439508A9064710D2@MBX06.ad.oak.ox.ac.uk</a>><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
Hi,<br>
<br>
I am trying to develop a plugin to do a custom export on our OMERO test server.<br>
<br>
Is there a recommended strategy for doing this? I am currently doing:<br>
<br>
1) Change plugin python code<br>
2) Refresh OMERO web page, and click on "Run scripts" > "Export Scripts" > "Test Export"<br>
3) Go to 1<br>
<br>
Which is quite a slow development cycle. It would be nice if I could run the script and pass the parameters to it on the command line somehow...<br>
<br>
I am using OMERO.web 5.0.6-ice34-b53.<br>
<br>
Thanks for any help!<br>
<br>
Steve<br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Fri, 1 May 2015 10:32:19 +0100<br>
From: William Moore <<a href="mailto:will@lifesci.dundee.ac.uk">will@lifesci.dundee.ac.uk</a>><br>
To: OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>><br>
Subject: Re: [ome-users] OMERO Scripts Plugins<br>
Message-ID:<br>
<<a href="mailto:D966E3A8-DDBA-4FF9-BD6F-37FBC0F7CD7C@lifesci.dundee.ac.uk">D966E3A8-DDBA-4FF9-BD6F-37FBC0F7CD7C@lifesci.dundee.ac.uk</a>><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
Hi Stephen,<br>
<br>
There are instructions for running scripts from the command line at<br>
<a href="https://www.openmicroscopy.org/site/support/omero5.1/developers/scripts/user-guide.html#run-script" target="_blank">https://www.openmicroscopy.org/site/support/omero5.1/developers/scripts/user-guide.html#run-script</a><br>
<br>
I also use the command line to replace scripts after each edit, since I'm editing them in a<br>
different location than bin/omero/scripts.<br>
But if your workflow doesn't need this then that's fine.<br>
<br>
One small 'hack' you can use to speed up testing in web is to copy the url of the<br>
script dialog, E.g. <a href="http://localhost:4080/webclient/script_ui/10656/?Image=3718" target="_blank">http://localhost:4080/webclient/script_ui/10656/?Image=3718</a><br>
and open a new window / tab and paste this url in, then run the script from here.<br>
Now, since the window.opener is no-longer the web client, the javascript that<br>
closes the script dialog when you run the script will fail and the dialog will stay open.<br>
Then you can simply refresh this window each time you update your script, which<br>
is quite a bit faster than re-opening it from web client each time.<br>
Results will still be shown in the web client if you refresh the Activities panel.<br>
<br>
Hope that helps,<br>
<br>
Will.<br>
<br>
<br>
<br>
On 1 May 2015, at 10:04, Stephen Taylor <<a href="mailto:stephen.taylor@imm.ox.ac.uk">stephen.taylor@imm.ox.ac.uk</a>> wrote:<br>
<br>
> Hi,<br>
><br>
> I am trying to develop a plugin to do a custom export on our OMERO test server.<br>
><br>
> Is there a recommended strategy for doing this? I am currently doing:<br>
><br>
> 1) Change plugin python code<br>
> 2) Refresh OMERO web page, and click on "Run scripts" > "Export Scripts" > "Test Export"<br>
> 3) Go to 1<br>
><br>
> Which is quite a slow development cycle. It would be nice if I could run the script and pass the parameters to it on the command line somehow...<br>
><br>
> I am using OMERO.web 5.0.6-ice34-b53.<br>
><br>
> Thanks for any help!<br>
><br>
> Steve<br>
><br>
><br>
> _______________________________________________<br>
> ome-users mailing list<br>
> <a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>
> <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
<br>
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<br>
Message: 5<br>
Date: Fri, 1 May 2015 10:44:43 +0000<br>
From: Stephen Taylor <<a href="mailto:stephen.taylor@imm.ox.ac.uk">stephen.taylor@imm.ox.ac.uk</a>><br>
To: OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>><br>
Subject: Re: [ome-users] OMERO Scripts Plugins<br>
Message-ID:<br>
<<a href="mailto:2574ACA6D1653848AAAE2E439508A906471327@MBX06.ad.oak.ox.ac.uk">2574ACA6D1653848AAAE2E439508A906471327@MBX06.ad.oak.ox.ac.uk</a>><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
Hi Will,<br>
<br>
That's great. Thanks for the tips!<br>
<br>
Steve<br>
<br>
From: ome-users [mailto:<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk">ome-users-bounces@lists.openmicroscopy.org.uk</a>] On Behalf Of William Moore<br>
Sent: 01 May 2015 10:32<br>
To: OME User Support List<br>
Subject: Re: [ome-users] OMERO Scripts Plugins<br>
<br>
Hi Stephen,<br>
<br>
There are instructions for running scripts from the command line at<br>
<a href="https://www.openmicroscopy.org/site/support/omero5.1/developers/scripts/user-guide.html#run-script" target="_blank">https://www.openmicroscopy.org/site/support/omero5.1/developers/scripts/user-guide.html#run-script</a><br>
<br>
I also use the command line to replace scripts after each edit, since I'm editing them in a<br>
different location than bin/omero/scripts.<br>
But if your workflow doesn't need this then that's fine.<br>
<br>
One small 'hack' you can use to speed up testing in web is to copy the url of the<br>
script dialog, E.g. <a href="http://localhost:4080/webclient/script_ui/10656/?Image=3718" target="_blank">http://localhost:4080/webclient/script_ui/10656/?Image=3718</a><br>
and open a new window / tab and paste this url in, then run the script from here.<br>
Now, since the window.opener is no-longer the web client, the javascript that<br>
closes the script dialog when you run the script will fail and the dialog will stay open.<br>
Then you can simply refresh this window each time you update your script, which<br>
is quite a bit faster than re-opening it from web client each time.<br>
Results will still be shown in the web client if you refresh the Activities panel.<br>
<br>
Hope that helps,<br>
<br>
Will.<br>
<br>
<br>
<br>
On 1 May 2015, at 10:04, Stephen Taylor <<a href="mailto:stephen.taylor@imm.ox.ac.uk">stephen.taylor@imm.ox.ac.uk</a><mailto:<a href="mailto:stephen.taylor@imm.ox.ac.uk">stephen.taylor@imm.ox.ac.uk</a>>> wrote:<br>
<br>
<br>
Hi,<br>
<br>
I am trying to develop a plugin to do a custom export on our OMERO test server.<br>
<br>
Is there a recommended strategy for doing this? I am currently doing:<br>
<br>
1) Change plugin python code<br>
2) Refresh OMERO web page, and click on "Run scripts" > "Export Scripts" > "Test Export"<br>
3) Go to 1<br>
<br>
Which is quite a slow development cycle. It would be nice if I could run the script and pass the parameters to it on the command line somehow...<br>
<br>
I am using OMERO.web 5.0.6-ice34-b53.<br>
<br>
Thanks for any help!<br>
<br>
Steve<br>
<br>
<br>
_______________________________________________<br>
ome-users mailing list<br>
<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><mailto:<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr"><div><font face="Times New Roman" size="3">
</font><font color="#000000" face="Times New Roman" size="3">
</font><p style="margin:0in 0in 0pt"><span style="color:rgb(31,73,125);font-family:"Arial","sans-serif";font-size:10pt"><font color="#000000">Jason
Miller, MD, PhD</font></span></p><p style="margin:0in 0in 0pt"><span style="color:rgb(31,73,125);font-family:"Arial","sans-serif";font-size:10pt"><font color="#000000">University of Michigan Kellogg Eye Center</font></span></p><p style="margin:0in 0in 0pt"><span style="color:rgb(31,73,125);font-family:"Arial","sans-serif";font-size:10pt"><font color="#000000">--</font></span></p><p style="margin:0in 0in 0pt"><span style="color:rgb(31,73,125);font-family:"Arial","sans-serif";font-size:10pt"><font color="#000000">Home address:<br></font></span></p><font color="#000000" face="Times New Roman" size="3">
</font><p style="margin:0in 0in 0pt"><span style="color:rgb(31,73,125);font-family:"Arial","sans-serif";font-size:10pt"><font color="#000000">117 Worden Ave<br></font></span></p><font color="#000000" face="Times New Roman" size="3">
</font><p style="margin:0in 0in 0pt"><span style="color:rgb(31,73,125);font-family:"Arial","sans-serif";font-size:10pt"><font color="#000000">Ann Arbor, MI 48103<br></font></span></p><font color="#000000" face="Times New Roman" size="3">
</font><p style="margin:0in 0in 0pt"><span style="color:rgb(31,73,125);font-family:"Arial","sans-serif";font-size:10pt"><font color="#000000">Cell: </font><a value="+14152252134"><font color="#000000">(415)
225-2134</font></a></span></p><font color="#000000" face="Times New Roman" size="3">
</font><p style="margin:0in 0in 0pt"><font color="#000000"><span style="color:rgb(31,73,125);font-family:"Arial","sans-serif";font-size:10pt">E-mail:
</span><b><span style="color:rgb(49,132,155);font-family:"Arial","sans-serif";font-size:10pt"><a href="mailto:jason.miller@stanfordalumni.org" target="_blank">jason.miller@stanfordalumni.org</a></span></b></font></p><p style="margin:0in 0in 0pt"><br><font color="#000000"><b><span style="color:rgb(49,132,155);font-family:"Arial","sans-serif";font-size:10pt"></span></b></font></p><p style="margin:0in 0in 0pt"><span style="color:rgb(31,73,125);font-family:"Arial","sans-serif";font-size:10pt"><font color="#000000">"When I was 5 years old, my mother always told me that happiness was the key to life. When I went to school, they asked me what I wanted to be when I grew up. I wrote down, 'Happy.' They told me I didn't understand the assignment. I told them they didn't understand life." - John Lennon<br></font></span></p><span href="http://www.quora.com/What-are-some-of-the-best-and-truest-life-quotes#"></span></div><div><div><font face="Times New Roman" size="3"></font></div></div></div></div>
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