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

[Maxime Woringer]

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).
-------------- next part --------------
A non-text attachment was scrubbed...
Name: BF007.nd2
Type: application/octet-stream
Size: 270336 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170813/cc4c296d/attachment-0003.obj>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: BF007.txt
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170813/cc4c296d/attachment-0002.txt>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: BF007-bf.tiff
Type: image/tiff
Size: 1337834 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170813/cc4c296d/attachment-0002.tiff>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: BF007-Capture du 2017-08-13 18-50-59.png
Type: image/png
Size: 53360 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170813/cc4c296d/attachment-0002.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: BF008.nd2
Type: application/octet-stream
Size: 294912 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170813/cc4c296d/attachment-0004.obj>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: BF008.txt
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170813/cc4c296d/attachment-0003.txt>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: BF008-bf.tiff
Type: image/tiff
Size: 470334 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170813/cc4c296d/attachment-0003.tiff>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: BF008-Capture du 2017-08-13 18-50-53.png
Type: image/png
Size: 61803 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170813/cc4c296d/attachment-0003.png>
-------------- next part --------------

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)
-------------- next part --------------
A non-text attachment was scrubbed...
Name: convert.log
Type: application/octet-stream
Size: 36351 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170813/cc4c296d/attachment-0005.obj>
-------------- next part --------------
- 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.
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 472 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170813/cc4c296d/attachment-0001.asc>