[ome-users] Two issues with ND2 (Nikon) files
Curtis Rueden
ctrueden at wisc.edu
Thu Aug 17 17:55:51 BST 2017
Hi Michael,
Recent versions of Bio-Formats require Java 7 or later, but your ImageJ is
still using Java 6.
For details on upgrading, see: https://imagej.net/Java_8
Regards,
Curtis
--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/
On Thu, Aug 17, 2017 at 10:45 AM, Cammer, Michael <
Michael.Cammer at med.nyu.edu> wrote:
> Please find below the error I get with the Aug 14 build of
> bioformats_package
>
>
>
>
>
> ImageJ 1.51p; Java 1.6.0_20 [64-bit]; Windows 7 6.1; 7794K of 12000MB (<1%)
>
> java.lang.UnsupportedClassVersionError: loci/plugins/LociImporter :
> Unsupported major.minor version 51.0
>
> at java.lang.ClassLoader.defineClass1(Native Method)
>
> at java.lang.ClassLoader.defineClassCond(ClassLoader.
> java:632)
>
> at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
>
> at java.security.SecureClassLoader.defineClass(
> SecureClassLoader.java:141)
>
> at java.net.URLClassLoader.defineClass(URLClassLoader.
> java:283)
>
> at java.net.URLClassLoader.access$000(URLClassLoader.
> java:58)
>
> at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
>
> at java.security.AccessController.doPrivileged(Native
> Method)
>
> at java.net.URLClassLoader.findClass(URLClassLoader.java:
> 190)
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
>
> at ij.IJ.runUserPlugIn(IJ.java:215)
>
> at ij.IJ.runPlugIn(IJ.java:181)
>
> at ij.IJ.runPlugIn(IJ.java:170)
>
> at HandleExtraFileTypes.openImage(
> HandleExtraFileTypes.java:258)
>
> at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)
>
> 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:514)
>
> at ij.io.Opener.openImage(Opener.java:368)
>
> at ij.io.Opener.openImage(Opener.java:242)
>
> at ij.io.Opener.open(Opener.java:109)
>
> at ij.io.Opener.openAndAddToRecent(Opener.java:291)
>
> at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:192)
>
> at ij.plugin.DragAndDrop.run(DragAndDrop.java:159)
>
> at java.lang.Thread.run(Thread.java:619)
>
>
>
>
>
> *Michael Cammer*
>
> Research Scientist
>
> DART Microscopy Laboratory
>
>
>
> *NYU Langone Health*
>
> 540 First Avenue
>
> SK2 Microscopy Suite
>
> New York, NY 10016
>
>
>
> C 914-309-3270 <(914)%20309-3270>
>
> Michael.Cammer at med.nyu.edu
>
> https://med.nyu.edu/research/research-resources/scientific-
> cores-shared-resources/microscopy-laboratory
>
> http://microscopynotes.com/
>
>
>
>
>
>
>
> *From:* ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] *On
> Behalf Of *David Gault (Staff)
> *Sent:* Wednesday, August 16, 2017 10:39 AM
>
> *To:* OME User Support List
> *Subject:* Re: [ome-users] Two issues with ND2 (Nikon) files
>
>
>
> Hi Michael and Maxime,
>
>
>
> Thank you for the further clarification and feedback on these issues.
>
>
>
> Michael, do you have a screenshot of the exception you were seeing with
> 5.6.0? Did it occur when opening any CZI image?
>
> If you had a sample file that was failing which you could upload to the
> below link that would be very useful for our testing:
>
> https://www.openmicroscopy.org/qa2/qa/upload/
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.openmicroscopy.org_qa2_qa_upload_&d=DQMFAg&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=LFOUtZvUoR4OJHDb8xi0B1ouJ2Lkr8dtNZGhMMmzZHo&s=N7IILdMFEgZ9CcSE-j5M-XsLdJC2DlI1Yl-r03zAbN8&e=>
>
>
>
> I have updated the Trello card with the additional detail and also with
> some details on further investigation into one of these issues:
>
> https://trello.com/c/RyXt2BAg/177-nd2-incorrect-channel-count
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__trello.com_c_RyXt2BAg_177-2Dnd2-2Dincorrect-2Dchannel-2Dcount&d=DQMFAg&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=LFOUtZvUoR4OJHDb8xi0B1ouJ2Lkr8dtNZGhMMmzZHo&s=W3JexGg4pOU9f1gelmO-i4Hjn2V6jLHSHY26r-VBv9E&e=>
>
>
>
> With Thanks,
>
> David Gault
>
>
>
> On 15 Aug 2017, at 20:17, Cammer, Michael <Michael.Cammer at med.nyu.edu>
> wrote:
>
>
>
> We are also having issues with CZI files with 5.6.0.
>
> The problem appears to be that when we click Stop during a timelapse
> experiment or if we move the stage while imaging, the images are not saved
> in the same CZI format as when we don't move the stage and let the
> experiment complete.
>
> This image
> http://microscopynotes.com/temp/bftemp/BioFormatsissue.png
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__microscopynotes.com_temp_bftemp_BioFormatsissue.png&d=DQMFAg&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=LFOUtZvUoR4OJHDb8xi0B1ouJ2Lkr8dtNZGhMMmzZHo&s=11jOOEH8c_ETwyrIBPydYEtEgwl1tquvgLMlzwS-mt0&e=>
> should be a simple color (AxioCam color) time series that fills the
> window. The sequences that went to completion open fine.
>
> We have been using 5.1.10-DEV built on 10 May 2016. Today we updated both
> ImageJ and BioFormats to the daily build and BioFormats always throws an
> exception. We rolled back to the the May 2010 version.
>
> Help appreciated.
>
> Thank you!
>
> Michael Cammer
> Research Scientist
> DART Microscopy Laboratory
>
> NYU Langone Health
> 540 First Avenue
> SK2 Microscopy Suite
> New York, NY 10016
>
> C 914-309-3270 <(914)%20309-3270>
> Michael.Cammer at med.nyu.edu
> https://med.nyu.edu/research/research-resources/scientific-
> cores-shared-resources/microscopy-laboratory
> http://microscopynotes.com/
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__microscopynotes.com_&d=DQMFAg&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=LFOUtZvUoR4OJHDb8xi0B1ouJ2Lkr8dtNZGhMMmzZHo&s=NQub4TDHShuVa8K3P0LhvNM0OIkaU4HfRRe1G5Zume8&e=>
>
>
>
>
> -----Original Message-----
> From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk
> <ome-users-bounces at lists.openmicroscopy.org.uk>] On Behalf Of Maxime
> Woringer
> Sent: Tuesday, August 15, 2017 1:08 PM
> To: OME User Support List
> Subject: Re: [ome-users] Two issues with ND2 (Nikon) files
>
> Hi David,
>
> I confirm that I also encounter the two issues mentioned below using the
> new BioFormats release (5.6.0).
>
> Best,
> Maxime
>
> David Gault (Staff) <d.gault at dundee.ac.uk> writes:
>
>
> Hi Maxime,
>
> Thank for reporting this issue and for providing sample files to test with.
> I can certainly reproduce the first the issue using the sample files
> provided and this does indeed look to be a bug.
> For the second issue I was unable to reproduce using bfconvert from the
> latest Bio-Formats release, and in theory the conversion should be the same
> as the FIJI result.
> Would you be able to run bfconvert -version to confirm that bftools is
> using the latest jars?
>
> I have created a Trello card on the Bio-Formats inbox for further
> investigation into these issues:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__trello.com_c_RyXt
> 2BAg_177-2Dnd2-2Dincorrect-2Dchannel-2Dcount&d=DQIBAg&c=j5oPpO0eBH1iio
> 48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_C
> qKkuo&m=g6CNr9rxiOItnhC2oaw8J5mhdFjCF0dh8hsaIy2xIHw&s=_XcwsqhVzEBCf-t1
> GTD086wg8D-d5f2UMVp16-f5bV8&e=
>
> With Thanks,
> David Gault
>
> On 14 Aug 2017, at 04:01, Maxime Woringer <maxime.woringer at berkeley.edu<
> mailto:maxime.woringer at berkeley.edu <maxime.woringer at berkeley.edu>>>
> wrote:
>
> Dear Bio-Formats users/developers,
>
> I am trying to convert ND2 files (acquired with NIkon NIS elements) to
> TIFF files, ideally in an automated fashion, but I am encountering
> issues that seem to me like bugs (but I'd be happy to be proven wrong).
>
> 1. Some single images appear corrupted when I try to convert them to
> TIFF. Below is an example. The two files (BF007 and BF008) were
> created on the same machine, same software, at a 30' interval. I am
> not aware of any differing setting except the ROI size.
> - BF008.nd2 opens properly in Fiji and converts properly using
> bfconvert (laters version). I am attaching the .nd2 file, the
> resulting TIFF file, and the convert log (.txt files) and a screenshot of
> how Fiji opens it.
> - BF008.nd2 opens corrupted in Fiji, and the same result happens using
> bfconvert. It seems that BF thinks it is a 3-channel image (it is not).
> <BF007.nd2><BF007.txt><BF007-bf.tiff><BF007-Capture du 2017-08-13
> 18-50-59.png><BF008.nd2><BF008.txt><BF008-bf.tiff><BF008-Capture du
> 2017-08-13 18-50-53.png> 2. Now moving to ND2 TIFF series (one
> channel, multiple timepoints), they open fine in Fiji using
> BioFormats, however, if I use the following
> command:
>
> bftools/bfconvert in.nd2 out.tiff
>
> The resulting TIFF file opens totally corrupted in Fiji/ImageJ (note
> that the first frame is fine).
>
> Below are an example source file (nd2), the conversion result using
> bfconvert, and the conversion result using Fiji. I am attaching the
> bfconvert log (convert.log)
> <convert.log>- Source ND2 file:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__cloud.biologie.en
> s.fr
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__s.fr_&d=DQMFAg&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=LFOUtZvUoR4OJHDb8xi0B1ouJ2Lkr8dtNZGhMMmzZHo&s=dk4HZH5s6iNWdSqklQk282ZO1Jzo8zFnYNRU3_Sipgk&e=>
> _index.php_s_H7OPHzLvJ3MPUkd&d=DQIBAg&c=j5oPpO0eBH1iio48DtsedbOBGm
> uw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=g6CN
> r9rxiOItnhC2oaw8J5mhdFjCF0dh8hsaIy2xIHw&s=tEBqotIUNL7T6mvP82ru7468tzwu
> CGWyMTZGnFSM0AY&e=
> - Corrupted TIFF generated by bfconvert:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__cloud.biologie.en
> s.fr
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__s.fr_&d=DQMFAg&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=LFOUtZvUoR4OJHDb8xi0B1ouJ2Lkr8dtNZGhMMmzZHo&s=dk4HZH5s6iNWdSqklQk282ZO1Jzo8zFnYNRU3_Sipgk&e=>
> _index.php_s_FFOIjHUg6Dl7B1I&d=DQIBAg&c=j5oPpO0eBH1iio48DtsedbOBGm
> uw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=g6CN
> r9rxiOItnhC2oaw8J5mhdFjCF0dh8hsaIy2xIHw&s=kw3iHYbQD1RC4jD2xAoqzFLatG0n
> crEdGR_BdVhwO9o&e=
> - Correct TIFF generated by Fiji:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__cloud.biologie.en
> s.fr
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__s.fr_&d=DQMFAg&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=LFOUtZvUoR4OJHDb8xi0B1ouJ2Lkr8dtNZGhMMmzZHo&s=dk4HZH5s6iNWdSqklQk282ZO1Jzo8zFnYNRU3_Sipgk&e=>
> _index.php_s_dyl1hZha3pGiP50&d=DQIBAg&c=j5oPpO0eBH1iio48DtsedbOBGm
> uw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=g6CN
> r9rxiOItnhC2oaw8J5mhdFjCF0dh8hsaIy2xIHw&s=mIZiSrvfdndBpDDckPsYvMtwh98W
> _Js7s8ZFy9OMIxg&e=
>
> Finally, I should mention that at least the latter issue happens with
> files generated with several versions of NIS elements.
>
> Am I the only person experiencing those issues? Is there any kind of
> additional information I should provide?
>
> - Version information: bf 5.5.3 and/or Fiji (latest update)
> - OS: I encounter the issue on Ubuntu 14.04 and Debian Jessie (8.9)
> - java version: I believe the one used is packaged by BioFormats, but
> in case, java -version returns
> Ubuntu machine:
> java version "1.8.0_144"
> Java(TM) SE Runtime Environment (build 1.8.0_144-b01)
> Java HotSpot(TM) 64-Bit Server VM (build 25.144-b01, mixed mode)
> Debian machine:
> java version "1.7.0_131"
> OpenJDK Runtime Environment (IcedTea 2.6.9) (7u131-2.6.9-2~deb8u1)
> OpenJDK 64-Bit Server VM (build 24.131-b00, mixed mode)
>
> Thanks a lot!
> Maxime
>
> PS: I tried to upload the files to the QA systemn, but it complains
> that my version of Flash is not up-to-date. I apologize about that and
> hope that you will be able to retrieve the files linked/attached.
> PPS: I have checked the "Common issues to check" page before sending
> this email, and I believe that none of them apply.
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