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

Wed Aug 16 15:39:21 BST 2017

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/

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

With Thanks,
David Gault

On 15 Aug 2017, at 20:17, Cammer, Michael <Michael.Cammer at med.nyu.edu<mailto: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
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<mailto: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<mailto: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><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<http://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<http://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<http://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.
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