[ome-users] multi-scene .czi files

Wed Aug 24 10:05:12 BST 2016

Excellent news. Thanks for all the work you and your colleagues do on this very important tool - it's much appreciated!

________________________________
From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk> on behalf of Sebastien Besson (Staff) <s.besson at dundee.ac.uk>
Sent: 24 August 2016 09:03:58
To: users OME
Subject: Re: [ome-users] multi-scene .czi files

Hi Oliver,

thanks for following up on this thread. The error you reported is expected as we did not
get this work finalized in time for Bio-Formats 5.2.0.

However, the bug fix for this CZI issues will be included in Bio-Formats 5.2.1 which we
expect to release on Thursday.

Best,
Sebastien

On 23 Aug 2016, at 11:50, Oliver Brookes <o.brookes at qmul.ac.uk<mailto:o.brookes at qmul.ac.uk>> wrote:

Hi Sebastien,

I've just updated to bioformats 5.2 in FIJI, but I'm still not able to open these .czi files. Error log looks pretty similar to before:

(Fiji Is Just) ImageJ 2.0.0-rc-49/1.51f; Java 1.8.0_66 [64-bit]; Windows 7 6.1; 33MB of 6009MB (<1%)

java.lang.NumberFormatException: null
at java.lang.Integer.parseInt(Integer.java:542)
at java.lang.Integer.parseInt(Integer.java:615)
at loci.formats.in.ZeissCZIReader.translateExperiment(ZeissCZIReader.java:2489)
at loci.formats.in.ZeissCZIReader.translateMetadata(ZeissCZIReader.java:1550)
at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:913)
at loci.formats.FormatReader.setId(FormatReader.java:1401)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:505)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)
at loci.plugins.in.Importer.showDialogs(Importer.java:140)
at loci.plugins.in.Importer.run(Importer.java:76)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:217)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:745)

Any word on when this might be fixed?

Thanks,

Oliver

________________________________
From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>> on behalf of Sebastien Besson (Staff) <s.besson at dundee.ac.uk<mailto:s.besson at dundee.ac.uk>>
Sent: 10 June 2016 23:29:14
To: users OME
Subject: Re: [ome-users] multi-scene .czi files

Hi Oliver,

we are currently working on finalising our model and API changes.
The current plan is to have 5.2.0 released by the end of the Summer.

Best,
Sebastien

On 8 Jun 2016, at 14:31, Oliver Brookes <o.brookes at qmul.ac.uk<mailto:o.brookes at qmul.ac.uk>> wrote:

Excellent, thanks for that. When is v5.2 likely to be released?

________________________________
From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>> on behalf of Sebastien Besson (Staff) <s.besson at dundee.ac.uk<mailto:s.besson at dundee.ac.uk>>
Sent: 08 June 2016 08:55:52
To: users OME
Subject: Re: [ome-users] multi-scene .czi files

Hi Oliver,

I can certainly reproduce your issue using Bio-Formats 5.1.10 and the file you
uploaded.

Note that a similar error to the one you described below has been reported in
https://github.com/openmicroscopy/bioformats/issues/2431 and we have a
bug fix proposed in https://github.com/openmicroscopy/bioformats/pull/2437 to
address it.

We will make sure your uploaded file is included as well for the testing of the
Pull Request. I would expect the bug fix to be released with Bio-Formats 5.2.0.

Best regards,
Sebastien

On 7 Jun 2016, at 17:51, Balaji Ramalingam (Staff) <b.ramalingam at dundee.ac.uk<mailto:b.ramalingam at dundee.ac.uk>> wrote:

Hi,

You can check your Bio-Formats version by selecting,
Help—>About Plugins—> Bio-Formats Plugins…

Or by running the following macro,
run("Bio-Formats Plugins...”);

We will check the files and get back to you at the earliest.
Hope that helps.

Best,
Balaji

__________________

Mr Balaji Ramalingam

Software Developer

OME Team

College of Life Sciences

University of Dundee

From: Oliver Brookes <o.brookes at qmul.ac.uk<mailto:o.brookes at qmul.ac.uk>>
Reply-To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Date: Tuesday, 7 June 2016 17:13
To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Subject: Re: [ome-users] multi-scene .czi files

Hi Sebastien,

I've uploaded one of my problem files. How do I check the bioformats version number please? I have the update site checked in the FIJI options, and I keep FIJI up to date, so I expect it to be the right version.

The images don't open. It throws an error message very similar to the one reported by Michael Cammer on the OME list in march of this year. My error log contents are:

(Fiji Is Just) ImageJ 2.0.0-rc-49/1.51a; Java 1.8.0_66 [64-bit]; Windows 7 6.1; 41MB of 6009MB (<1%)

java.lang.NumberFormatException: null
at java.lang.Integer.parseInt(Integer.java:542)
at java.lang.Integer.parseInt(Integer.java:615)
at loci.formats.in.ZeissCZIReader.translateExperiment(ZeissCZIReader.java:2268)
at loci.formats.in.ZeissCZIReader.translateMetadata(ZeissCZIReader.java:1329)
at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:731)
at loci.formats.FormatReader.setId(FormatReader.java:1426)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:505)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)
at loci.plugins.in.Importer.showDialogs(Importer.java:140)
at loci.plugins.in.Importer.run(Importer.java:76)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:216)
at ij.IJ.runPlugIn(IJ.java:180)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:745)

Let me just clarify that this only happens on multi-position images. Normal images, stacks and videos open fine. When I hover the mouse over the files that won't open (in windows 7), or look at their properties, they all have XYCZTSB dimensions, but the ones that will open all only have XYCZT. If I use the zen software to split the images into individual scenes, the scenes still retain the XYCZTSB, although S and B now always have a value of 1, and they still fail to open and throw the error message.

Thanks for looking into this,

Oliver

________________________________
From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>> on behalf of Sebastien Besson (Staff) <s.besson at dundee.ac.uk<mailto:s.besson at dundee.ac.uk>>
Sent: 06 June 2016 11:02:00
To: users OME
Subject: Re: [ome-users] multi-scene .czi files

Hi Oliver,

the Zeiss scene dimension should be supported by Bio-Formats and we certainly have
several representative CZI datasets including multiple scenes tested daily.

Could you first of all confirm you are using Bio-Formats 5.1.10 in Fiji? Also, can you give us
more detail about the issue: is an error thrown by Bio-Formats when opening the file or is a
single position opened with wrong dimensions? Finally do you have a sample file that you could
upload to http://qa.openmicroscopy.org.uk/qa/upload/ to reproduce the issue?

Best,
Sebastien

On 2 Jun 2016, at 10:25, Oliver Brookes <o.brookes at qmul.ac.uk<mailto:o.brookes at qmul.ac.uk>> wrote:

Hello, I've found that it's not possible to open multiple scene Zeiss images using bioformats in FIJI. Using the "positions" option on our Zeiss Elyra, it's possible to store multiple locations and automatically take pictures (very good for timelapse video). The positional info is stored in the .czi format as a "scene" dimension - the dimensions of the file are listed as XYCZTSB. I can open czi images, stacks and movies that are taken at single positions (anything where the dimensions of the .czi file are XYCZT). Is the extended .czi format not supported?

Thanks,

Oliver

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The University of Dundee is a registered Scottish Charity, No: SC015096

The University of Dundee is a registered Scottish Charity, No: SC015096
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The University of Dundee is a registered Scottish Charity, No: SC015096
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ome-users at lists.openmicroscopy.org.uk<mailto: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
_______________________________________________
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