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

[Maxime Woringer]

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> 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> 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>> 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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