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

[David Gault (Staff)]

Hi Maxime,

Thank you for testing and confirming this is still an issue. Unfortunately we were unable to put in place a fix for this specific issue in time for the latest release.
I have opened a PR to begin testing and reviewing a fix for this issue in a future release.
https://github.com/openmicroscopy/bioformats/pull/2966

With Thanks,
David Gault

On 20 Sep 2017, at 16:21, Maxime Woringer <maxime.woringer at berkeley.edu<mailto:maxime.woringer at berkeley.edu>> wrote:

Hi David,

I confirm that I still encounter the first issue mentioned (wrong
channel count) in the latest Bio-Formats release (5.7.1).

Best,
Maxime

Maxime Woringer <maxime.woringer at berkeley.edu<mailto:maxime.woringer at berkeley.edu>> writes:
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://trello.com/c/RyXt2BAg/177-nd2-incorrect-channel-count

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://cloud.biologie.ens.fr/index.php/s/H7OPHzLvJ3MPUkd
- Corrupted TIFF generated by bfconvert: https://cloud.biologie.ens.fr/index.php/s/FFOIjHUg6Dl7B1I
- Correct TIFF generated by Fiji: https://cloud.biologie.ens.fr/index.php/s/dyl1hZha3pGiP50

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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