[ome-users] Saving large files in ome.tif or ids/ics
Jason Miller
scientistmiller at gmail.com
Sat May 2 00:48:11 BST 2015
Hi Roger-
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.
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? scientistmiller at gmail.com.
Thanks so very much for your help.
-Jason
On Fri, May 1, 2015 at 7:00 AM, <
ome-users-request at lists.openmicroscopy.org.uk> wrote:
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> Today's Topics:
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> 1. Re: Saving large files in ome.tif or ids/ics (Roger Leigh)
> 2. One week left to register for the Paris Users Meeting!
> (Helen Flynn (Staff))
> 3. OMERO Scripts Plugins (Stephen Taylor)
> 4. Re: OMERO Scripts Plugins (William Moore)
> 5. Re: OMERO Scripts Plugins (Stephen Taylor)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 1 May 2015 08:50:49 +0000
> From: Roger Leigh <r.leigh at dundee.ac.uk>
> To: <ome-users at lists.openmicroscopy.org.uk>
> Subject: Re: [ome-users] Saving large files in ome.tif or ids/ics
> Message-ID: <55433E69.5060100 at dundee.ac.uk>
> Content-Type: text/plain; charset="windows-1252"; format=flowed
>
> On 30/04/2015 21:40, Jason Miller wrote:
>
> Dear Jason,
>
> > Similar to recent past posts on this list, I'm having trouble saving
> > files that are > 4GB into ome.tif or IDS/ICS formats. I have a 5GB file,
> > open as a virtual file, and when I go to export via Bioformats Exporter
> > to IDS/ICS format, I get the following error:
> [stacktrace]
>
> For IDS/ICS, this was fixed in this PR last week:
> https://github.com/openmicroscopy/bioformats/pull/1738
> I have tested this with >5GB images and it works correctly.
>
> > When I go to export to ome.tif format, I get the same error previously
> > reported on this list:
> > loci.formats.FormatException: File is too large; call setBigTiff(true)
> >
> > Is it possible to retain the ome.tif format for >4GB? In my case, this
> > is for importing into Huygens for deconvolution.
>
> For plain (not OME) TIFF:
> https://github.com/openmicroscopy/bioformats/pull/1744
>
> Both of the above fixes are in the newly-released Bio-Formats 5.1.1
> release. If using Fiji, you should automatically get this update; for
> ImageJ you can download the updated plugin from
> http://downloads.openmicroscopy.org/bio-formats/5.1.1/
>
> For OME-TIFF, it's not currently possible to enable BigTIFF when
> exporting from ImageJ using the exporter dialogue. For the plain TIFF
> case, rather than relying on an API call to enable BigTIFF, we now
> enable it if the image data is >4GiB or a "big" TIFF file extension such
> as .btf, .tf8 or .tf2 is used. We would like to do the same for
> OME-TIFF, but this first requires updating the OME-TIFF specification
> which currently only allows a .ome.tiff or .ome.tif file extension.
> Once that's done, you would be able to use e.g. ".ome.btf" and get a
> "big" OME-TIFF file. However, this does require some consideration
> since (for example) these files would not be readable with older
> versions of Bio-Formats unless you renamed them to ".ome.tiff" after
> export.
>
> To summarise, it isn't currently possible to export >4GB ome.tiff files
> using the Bio-Formats Exporter. It is possible via the Java API by
> calling writer.setBigTiff(true) if this is an option for you. This is a
> known limitation which we are working on; see the discussion in the PR
> #1744 above.
>
> There is a ticket open here for this:
> https://trac.openmicroscopy.org/ome/ticket/12858
> I can add you as a CC on it if you like, so you'll be kept up to date
> with its progress?
>
>
> Kind 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
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 1 May 2015 08:56:58 +0000
> From: "Helen Flynn (Staff)" <h.flynn at dundee.ac.uk>
> To: "<ome-users at lists.openmicroscopy.org.uk>"
> <ome-users at lists.openmicroscopy.org.uk>,
> "<ome-devel at lists.openmicroscopy.org.uk>"
> <ome-devel at lists.openmicroscopy.org.uk>
> Subject: [ome-users] One week left to register for the Paris Users
> Meeting!
> Message-ID: <DDCB0DD8-60C6-4A22-B65C-C34B1C6DBC62 at dundee.ac.uk>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear All,
>
> 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.
>
> The programme is up at
> https://www.openmicroscopy.org/site/community/minutes/meetings/10th-annual-users-meeting-june-2015
> and you can book via
>
> http://www.buyat.dundee.ac.uk/browse/extra_info.asp?compid=1&modid=2&catid=62&prodid=437
>
> 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!
>
> Regards,
>
> The OME Team
>
> Dr Helen Flynn
> OME Technical Writer
> Centre for Gene Regulation & Expression
> Open Microscopy Environment
> University of Dundee
> http://openmicroscopy.org<http://openmicroscopy.org/>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
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> ------------------------------
>
> Message: 3
> Date: Fri, 1 May 2015 09:04:01 +0000
> From: Stephen Taylor <stephen.taylor at imm.ox.ac.uk>
> To: "ome-users at lists.openmicroscopy.org.uk"
> <ome-users at lists.openmicroscopy.org.uk>
> Subject: [ome-users] OMERO Scripts Plugins
> Message-ID:
> <2574ACA6D1653848AAAE2E439508A9064710D2 at MBX06.ad.oak.ox.ac.uk>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
> I am trying to develop a plugin to do a custom export on our OMERO test
> server.
>
> Is there a recommended strategy for doing this? I am currently doing:
>
> 1) Change plugin python code
> 2) Refresh OMERO web page, and click on "Run scripts" > "Export Scripts"
> > "Test Export"
> 3) Go to 1
>
> 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...
>
> I am using OMERO.web 5.0.6-ice34-b53.
>
> Thanks for any help!
>
> Steve
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 1 May 2015 10:32:19 +0100
> From: William Moore <will at lifesci.dundee.ac.uk>
> To: OME User Support List <ome-users at lists.openmicroscopy.org.uk>
> Subject: Re: [ome-users] OMERO Scripts Plugins
> Message-ID:
> <D966E3A8-DDBA-4FF9-BD6F-37FBC0F7CD7C at lifesci.dundee.ac.uk>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Stephen,
>
> There are instructions for running scripts from the command line at
>
> https://www.openmicroscopy.org/site/support/omero5.1/developers/scripts/user-guide.html#run-script
>
> I also use the command line to replace scripts after each edit, since I'm
> editing them in a
> different location than bin/omero/scripts.
> But if your workflow doesn't need this then that's fine.
>
> One small 'hack' you can use to speed up testing in web is to copy the url
> of the
> script dialog, E.g.
> http://localhost:4080/webclient/script_ui/10656/?Image=3718
> and open a new window / tab and paste this url in, then run the script
> from here.
> Now, since the window.opener is no-longer the web client, the javascript
> that
> closes the script dialog when you run the script will fail and the dialog
> will stay open.
> Then you can simply refresh this window each time you update your script,
> which
> is quite a bit faster than re-opening it from web client each time.
> Results will still be shown in the web client if you refresh the
> Activities panel.
>
> Hope that helps,
>
> Will.
>
>
>
> On 1 May 2015, at 10:04, Stephen Taylor <stephen.taylor at imm.ox.ac.uk>
> wrote:
>
> > Hi,
> >
> > I am trying to develop a plugin to do a custom export on our OMERO test
> server.
> >
> > Is there a recommended strategy for doing this? I am currently doing:
> >
> > 1) Change plugin python code
> > 2) Refresh OMERO web page, and click on "Run scripts" > "Export
> Scripts" > "Test Export"
> > 3) Go to 1
> >
> > 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...
> >
> > I am using OMERO.web 5.0.6-ice34-b53.
> >
> > Thanks for any help!
> >
> > Steve
> >
> >
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
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> ------------------------------
>
> Message: 5
> Date: Fri, 1 May 2015 10:44:43 +0000
> From: Stephen Taylor <stephen.taylor at imm.ox.ac.uk>
> To: OME User Support List <ome-users at lists.openmicroscopy.org.uk>
> Subject: Re: [ome-users] OMERO Scripts Plugins
> Message-ID:
> <2574ACA6D1653848AAAE2E439508A906471327 at MBX06.ad.oak.ox.ac.uk>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Will,
>
> That's great. Thanks for the tips!
>
> Steve
>
> From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On
> Behalf Of William Moore
> Sent: 01 May 2015 10:32
> To: OME User Support List
> Subject: Re: [ome-users] OMERO Scripts Plugins
>
> Hi Stephen,
>
> There are instructions for running scripts from the command line at
>
> https://www.openmicroscopy.org/site/support/omero5.1/developers/scripts/user-guide.html#run-script
>
> I also use the command line to replace scripts after each edit, since I'm
> editing them in a
> different location than bin/omero/scripts.
> But if your workflow doesn't need this then that's fine.
>
> One small 'hack' you can use to speed up testing in web is to copy the url
> of the
> script dialog, E.g.
> http://localhost:4080/webclient/script_ui/10656/?Image=3718
> and open a new window / tab and paste this url in, then run the script
> from here.
> Now, since the window.opener is no-longer the web client, the javascript
> that
> closes the script dialog when you run the script will fail and the dialog
> will stay open.
> Then you can simply refresh this window each time you update your script,
> which
> is quite a bit faster than re-opening it from web client each time.
> Results will still be shown in the web client if you refresh the
> Activities panel.
>
> Hope that helps,
>
> Will.
>
>
>
> On 1 May 2015, at 10:04, Stephen Taylor <stephen.taylor at imm.ox.ac.uk
> <mailto:stephen.taylor at imm.ox.ac.uk>> wrote:
>
>
> Hi,
>
> I am trying to develop a plugin to do a custom export on our OMERO test
> server.
>
> Is there a recommended strategy for doing this? I am currently doing:
>
> 1) Change plugin python code
> 2) Refresh OMERO web page, and click on "Run scripts" > "Export Scripts"
> > "Test Export"
> 3) Go to 1
>
> 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...
>
> I am using OMERO.web 5.0.6-ice34-b53.
>
> Thanks for any help!
>
> Steve
>
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk<mailto:
> ome-users at lists.openmicroscopy.org.uk>
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
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> ------------------------------
>
> End of ome-users Digest, Vol 122, Issue 2
> *****************************************
>
--
Jason Miller, MD, PhD
University of Michigan Kellogg Eye Center
--
Home address:
117 Worden Ave
Ann Arbor, MI 48103
Cell: (415) 225-2134
E-mail: *jason.miller at stanfordalumni.org <jason.miller at stanfordalumni.org>*
"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
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