[ome-users] Two issues with ND2 (Nikon) files

Tue Aug 15 20:17:56 BST 2017

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
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
Michael.Cammer at med.nyu.edu
https://med.nyu.edu/research/research-resources/scientific-cores-shared-resources/microscopy-laboratory
http://microscopynotes.com/ 

-----Original Message-----
From: ome-users [mailto: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>> 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_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_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_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.
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicro
> scopy.org.uk> 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.openmicrosco
> py.org.uk_mailman_listinfo_ome-2Dusers&d=DQIBAg&c=j5oPpO0eBH1iio48Dtse
> dbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&
> m=g6CNr9rxiOItnhC2oaw8J5mhdFjCF0dh8hsaIy2xIHw&s=E7dtZPSuF8MP-R8RXQ4wOJ
> Mw2gRIbrDQO2VivlBdGD8&e=
>
>
> The University of Dundee is a registered Scottish Charity, No: 
> SC015096 _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.openmicrosco
> py.org.uk_mailman_listinfo_ome-2Dusers&d=DQIBAg&c=j5oPpO0eBH1iio48Dtse
> dbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&
> m=g6CNr9rxiOItnhC2oaw8J5mhdFjCF0dh8hsaIy2xIHw&s=E7dtZPSuF8MP-R8RXQ4wOJ
> Mw2gRIbrDQO2VivlBdGD8&e=

------------------------------------------------------------
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
=================================