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

Mon Sep 4 17:53:23 BST 2017

Hi David,

Thank you very much for this follow-up. I will follow the progress on
the Trello card.

I confirm that the two bugs still occur in BF5.7.0. I can't tell how
excited I am to read that you identified where the issue comes from!
Actually, I found out that people have been annoyed by these ND2
conversion "issues" since at least 2013 (no idea why nobody reported it,
though). 

Regarding the second issue, I am getting more and more confused:
- When I import the resulting TIFF file into Fiji with File -> Open
(without the Bio-Formats importer), all the frame, starting at frame 2,
appear corrupted (I am attaching a screenshot of frame 2)
- When I use the Bio-Formats importer, then the TIFF file imports just
fine.

This suggest that I am missing something obvious... Can't the TIFF
files produced by bfconvert be read natively by ImageJ?

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Thanks a lot,
Maxime

David Gault (Staff) <d.gault at dundee.ac.uk> writes:

> Hi Maxime,
>
> We have been able to further debug the first issue to identify how the problem occurs but we do not yet have a fix in place for it.
> You can follow the progress of that issue on the Trello card here: https://trello.com/c/RyXt2BAg/177-nd2-incorrect-channel-count
>
> With regards the second issue I have still been unable to reproduce it. If I open the 2 converted files you had originally attached (one converted with bfconvert, the other with FIJI) both open and display the same when using the latest FIJI install.
> When you converted the TIFF image using FIJI, and when you read the image back, was that using the Bio-Formats exporter and importer?
>
> With Thanks,
> David Gault
>
> On 1 Sep 2017, at 18:59, Maxime Woringer <maxime.woringer at berkeley.edu<mailto:maxime.woringer at berkeley.edu>> wrote:
>
> Hi David,
>
> Do you have any update about the two bugs mentioned earlier? Were you
> able to reproduce the second bug mentioned in my previous email?
>
> Thanks a lot,
> 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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