[ome-users] ome-users Digest, Vol 138, Issue 1

Fri Sep 2 10:26:24 BST 2016

Dear Bio-Formats and OME-team,

It is really awesome that JPEG XR support is coming to Bio-Formats! Thank you (and Zeiss) so much for making this happen!
It is a huge improvement for groups or facilities that are using the Zeiss slide scanner or other systems generating JPEG XR.
Thank you for listening to us and our problems!

Cheers,
Oliver

Oliver Biehlmaier, PhD | Head of Imaging Core Facility  | Biozentrum, University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel
Phone: +41 61 267 20 73 | Email: oliver.biehlmaier at unibas.ch<mailto:oliver.biehlmaier at unibas.ch> | www.biozentrum.unibas.ch/imcf<http://www.biozentrum.unibas.ch/imcf> | www.microscopynetwork.unibas.ch<http://www.microscopynetwork.unibas.ch>

On 01 Sep 2016, at 13:00, ome-users-request at lists.openmicroscopy.org.uk<mailto:ome-users-request at lists.openmicroscopy.org.uk> wrote:

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Today's Topics:

  1. Re: JPEG XR compression support is coming to Bio-Formats
     (Jason Swedlow (Staff))
  2. Re: Fiji error - opening certain .czi files (David Gault (Staff))

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Message: 1
Date: Wed, 31 Aug 2016 11:43:40 +0000
From: "Jason Swedlow (Staff)" <j.r.swedlow 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: Re: [ome-users] JPEG XR compression support is coming to
Bio-Formats
Message-ID:
<DB5PR04MB206972F592FE86F2875C804A94E30 at DB5PR04MB2069.eurprd04.prod.outlook.com>

Content-Type: text/plain; charset="windows-1252"

Dear All-

Just to follow up on this? as you probably gleaned from Helen?s email, we?ve been pursuing several ways to fund the many aspects of our work so we can deliver the tools and resources the community needs. Some of these are in standard grants- more about recent progress in funding OME in an upcoming email. Some involve collaborations with industrial partners; others involve specific projects and applications (the BBSRC-funded IDR is an example of this).

Today?s entry in the OME blog (http://blog.openmicroscopy.org/file-formats/community/2016/08/31/bf-partnerships/) discusses examples of ways we are working with industrial partners to ensure that the range of tools and capabilities required by the community are delivered. The blog describes two examples of working with commercial imaging companies, namely 3i and ZEISS Microscopy, to deliver readers for Bio-Formats. File formats readers are particularly challenging to fund, for obvious reasons.  With 3i and ZEISS, we?ve come up with creative ways to deliver work the community needs. We hope these serve as examples and templates for further collaborations with the industrial imaging community. Our thanks to 3i and ZEISS for their open and forward-looking approach to delivering solutions for the community of imaging scientists.

We welcome feedback and ideas from the OME user and developer community on these issues.  Overall, we must diversify our funding sources.  More about the broader funding strategy in a future email.

As always, thanks for your support.

Cheers,

Jason

----------------------
Centre for Gene Regulation & Expression | Open Microscopy Environment | University of Dundee

Phone:  +44 (0) 1382 385819
email: j.swedlow at dundee.ac.uk<https://dbxprd0410.outlook.com/owa/redir.aspx?C=XlY__cjOnUCLrUuc7zPnSr5hht0k884Icce5AfHAhv6fHZjWmwxAigQ84T9_MIRi02LghCy2-Tk.&URL=mailto%3aj.swedlow%40dundee.ac.uk>

Web: http://www.lifesci.dundee.ac.uk/people/jason-swedlow<https://dbxprd0410.outlook.com/owa/redir.aspx?C=XlY__cjOnUCLrUuc7zPnSr5hht0k884Icce5AfHAhv6fHZjWmwxAigQ84T9_MIRi02LghCy2-Tk.&URL=http%3a%2f%2fwww.lifesci.dundee.ac.uk%2fgre%2fstaff%2fjason-swedlow>
Open Microscopy Environment: http://openmicroscopy.org<https://dbxprd0410.outlook.com/owa/redir.aspx?C=XlY__cjOnUCLrUuc7zPnSr5hht0k884Icce5AfHAhv6fHZjWmwxAigQ84T9_MIRi02LghCy2-Tk.&URL=http%3a%2f%2fopenmicroscopy.org>

________________________________
From: ome-devel <ome-devel-bounces at lists.openmicroscopy.org.uk> on behalf of Helen Flynn (Staff) <h.flynn at dundee.ac.uk>
Sent: Tuesday, August 30, 2016 2:01:02 PM
To: ome-users at lists.openmicroscopy.org.uk; ome-devel at lists.openmicroscopy.org.uk
Subject: [ome-devel] JPEG XR compression support is coming to Bio-Formats

Dear All,

We are delighted to announce that thanks to a collaboration between Glencoe Software and Carl Zeiss Microscopy GmbH, support for whole slide images compressed with the JPEG XR compression scheme is coming to Bio-Formats.

Jason Swedlow says "We are particularly excited that the software we build in this collaboration will be available for anyone to download and use. This is a great example of how industrial partners can work together and build important capabilities that benefit the global scientific and pathology imaging communities. The work we do together will benefit users of ZEISS Axio Scan.Z1 and indeed anyone who uses JPEG XR compression in their image data."

This development will allow researchers, pathologists and imaging specialists working with these images worldwide to use a whole range of open source tools that rely on Bio-Formats for image file translation.

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

The University of Dundee is a registered Scottish Charity, No: SC015096
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Message: 2
Date: Wed, 31 Aug 2016 14:28:47 +0000
From: "David Gault (Staff)" <d.gault at dundee.ac.uk>
To: OME User Support List <ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] Fiji error - opening certain .czi files
Message-ID: <2B467ED9-1D24-43CF-9F86-08A33092E797 at dundee.ac.uk>
Content-Type: text/plain; charset="iso-8859-1"

Hi Cecilia,

Thank you for sending this report, we also received the sample file you sent via QA and have since tested it and were able to reproduce the same error that you discovered.
This error appears to be related to an existing issue for which we have a bug tracking ticket - https://trac.openmicroscopy.org/ome/ticket/13239

I have updated the ticket to with this information as well as the sample QA file which you provided for testing.

With Thanks,
David Gault

On 31 Aug 2016, at 09:29, Dom?nguez Conde Cecilia <Cecilia.DominguezConde at rud.lbg.ac.at<mailto:Cecilia.DominguezConde at rud.lbg.ac.at>> wrote:

Dear all,

I want to report an error in Fiji when trying to open certain .czi files (I tried uploading a 62MB file to your QA system but did not succeed, let me know if I should send it via FTP server, although from the size QA should have worked).

Error message below.

Looking forward to your feedback and thank you in advance,
Cecilia

ERROR MESSAGE:

[ERROR] Exception during event handling:
[Event] org.scijava.platform.event.AppOpenFilesEvent
context = org.scijava.Context at 4a0de467
consumed = false
[Subscriber] net.imagej.legacy.IJ1Helper$LegacyEventDelegator at 7ba63fe5
[Method] private void net.imagej.legacy.IJ1Helper$LegacyEventDelegator.onEvent(org.scijava.platform.event.AppOpenFilesEvent)
java.lang.IllegalArgumentException: Invalid C index: 1/1
at loci.formats.FormatTools.getIndex(FormatTools.java:413)
at loci.formats.FormatTools.getIndex(FormatTools.java:340)
at loci.formats.FormatReader.getIndex(FormatReader.java:1113)
at loci.formats.in.ZeissCZIReader.assignPlaneIndices(ZeissCZIReader.java:1296)
at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:773)
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:217)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.IJ.runPlugIn(IJ.java:170)
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
at ij.IJ.runUserPlugIn(IJ.java:217)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.IJ.runPlugIn(IJ.java:170)
at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:515)
at ij.io.Opener.openImage(Opener.java:369)
at ij.io.Opener.openImage(Opener.java:243)
at ij.io.Opener.open(Opener.java:110)
at ij.io.Opener.openAndAddToRecent(Opener.java:292)
at net.imagej.legacy.IJ1Helper.openAndAddToRecent(IJ1Helper.java:465)
at net.imagej.legacy.IJ1Helper$LegacyEventDelegator.onEvent(IJ1Helper.java:591)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.scijava.event.DefaultEventService$ProxySubscriber.onEvent(DefaultEventService.java:302)
at org.scijava.event.DefaultEventService$ProxySubscriber.onEvent(DefaultEventService.java:276)
at org.bushe.swing.event.ThreadSafeEventService.publish(ThreadSafeEventService.java:971)
at org.scijava.event.DefaultEventBus.access$101(DefaultEventBus.java:56)
at org.scijava.event.DefaultEventBus$1.run(DefaultEventBus.java:190)
at org.scijava.thread.DefaultThreadService.invoke(DefaultThreadService.java:107)
at org.scijava.event.DefaultEventBus.publishNow(DefaultEventBus.java:184)
at org.scijava.event.DefaultEventBus.publishNow(DefaultEventBus.java:75)
at org.scijava.event.DefaultEventService.publish(DefaultEventService.java:104)
at org.scijava.plugins.platforms.osx.OSXAppEventDispatcher.openFiles(OSXAppEventDispatcher.java:205)
at com.apple.eawt._AppEventHandler$_OpenFileDispatcher.performUsing(_AppEventHandler.java:361)
at com.apple.eawt._AppEventHandler$_OpenFileDispatcher.performUsing(_AppEventHandler.java:352)
at com.apple.eawt._AppEventHandler$_AppEventDispatcher$1.run(_AppEventHandler.java:516)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
[ERROR] Exception during event handling:
[Event] org.scijava.platform.event.AppOpenFilesEvent
context = org.scijava.Context at 4a0de467
consumed = false
[Subscriber] net.imagej.legacy.IJ1Helper$LegacyEventDelegator at 7ba63fe5
[Method] private void net.imagej.legacy.IJ1Helper$LegacyEventDelegator.onEvent(org.scijava.platform.event.AppOpenFilesEvent)
java.lang.IllegalArgumentException: Invalid C index: 1/1
at loci.formats.FormatTools.getIndex(FormatTools.java:413)
at loci.formats.FormatTools.getIndex(FormatTools.java:340)
at loci.formats.FormatReader.getIndex(FormatReader.java:1113)
at loci.formats.in.ZeissCZIReader.assignPlaneIndices(ZeissCZIReader.java:1296)
at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:773)
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:217)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.IJ.runPlugIn(IJ.java:170)
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
at ij.IJ.runUserPlugIn(IJ.java:217)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.IJ.runPlugIn(IJ.java:170)
at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:515)
at ij.io.Opener.openImage(Opener.java:369)
at ij.io.Opener.openImage(Opener.java:243)
at ij.io.Opener.open(Opener.java:110)
at ij.io.Opener.openAndAddToRecent(Opener.java:292)
at net.imagej.legacy.IJ1Helper.openAndAddToRecent(IJ1Helper.java:465)
at net.imagej.legacy.IJ1Helper$LegacyEventDelegator.onEvent(IJ1Helper.java:591)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.scijava.event.DefaultEventService$ProxySubscriber.onEvent(DefaultEventService.java:302)
at org.scijava.event.DefaultEventService$ProxySubscriber.onEvent(DefaultEventService.java:276)
at org.bushe.swing.event.ThreadSafeEventService.publish(ThreadSafeEventService.java:971)
at org.scijava.event.DefaultEventBus.access$101(DefaultEventBus.java:56)
at org.scijava.event.DefaultEventBus$1.run(DefaultEventBus.java:190)
at org.scijava.thread.DefaultThreadService.invoke(DefaultThreadService.java:107)
at org.scijava.event.DefaultEventBus.publishNow(DefaultEventBus.java:184)
at org.scijava.event.DefaultEventBus.publishNow(DefaultEventBus.java:75)
at org.scijava.event.DefaultEventService.publish(DefaultEventService.java:104)
at org.scijava.plugins.platforms.osx.OSXAppEventDispatcher.openFiles(OSXAppEventDispatcher.java:205)
at com.apple.eawt._AppEventHandler$_OpenFileDispatcher.performUsing(_AppEventHandler.java:361)
at com.apple.eawt._AppEventHandler$_OpenFileDispatcher.performUsing(_AppEventHandler.java:352)
at com.apple.eawt._AppEventHandler$_AppEventDispatcher$1.run(_AppEventHandler.java:516)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

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