[ome-users] Bio-Formats ND2 importer bug

[Stephane Dallongeville]

Hi David,

Thanks for your prompt reply and for providing tips about how to open 
the image :)
We are also looking for the fix as in Icy we don't provide access to 
Bio-Formats advanced options for users ;)

Best regards,

- Stephane


Le 08/02/2018 à 11:44, David Gault (Staff) a écrit :
>
> Hi Stephane,
>
> Thanks for getting in touch and providing a sample file allowing to 
> reproduce. I can definitely confirm that with the latest Bio-Formats 
> release only a single image is read and that exceptions are reported 
> with previous versions. Bio-Formats has recently introduced an option 
> in the Nikon ND2 reader to make use of the available chunkmap in order 
> to speed up the reader initialization notably for very large Nikon ND2 
> files.  Although this change has been tested against all Nikon ND2 
> files in our data repository, we have received reports 
> of issues caused by this change. We are continuing to make 
> improvements to this behaviour but as an immediate workaround, 
> disabling the chunkmap processing should restore the correct 
> dimensionality.
>
> In FIJI you can do this by disabling the following option:
>
> Plugins -> Bio-Formats -> Bio-Formats Plugins Configuration -> Formats 
> -> Nikon ND2 -> Disable Chunkmap option
>
>
> Or using the Bio-Fomrats Java library you can disable it as below:
>
> DynamicMetadataOptions options = new DynamicMetadataOptions();
> options.setBoolean("nativend2.chunkmap", false);
> reader.setMetadataOptions(options);
>
>
> With Thanks,
> David Gault
>
>> On 7 Feb 2018, at 14:37, Stephane Dallongeville 
>> <stephane.dallongeville at pasteur.fr 
>> <mailto:stephane.dallongeville at pasteur.fr>> wrote:
>>
>> Dear Bio-Formats team,
>>
>> One of our users reported an issue while opening a .ND2 file you can 
>> find here :
>>
>> https://drive.google.com/file/d/1DL51ncu83ET_VQgCEXDW5j6bY0jET_XX/view?usp=sharing
>>
>> The dataset is supposed to be a time lapse but with recents 
>> Bio-formats releases it opens as a single image (sizeT = 1).
>> I tested with older bio-formats versions (mayeb 2 year ago) and the 
>> dataset was opening correctly (complete timelaps)
>> With some more recents versions (1 year ago) the ND2 reader was 
>> throwing a Negative Index Exception.
>>
>> Hope it helps to fix the issue :)
>>
>> Best,
>>
>> -- 
>> Stephane Dallongeville
>> Unité d'Analyse d'Images Biologiques
>> CNRS UMR 3691
>> Institut Pasteur
>> 25 rue du Dr. Roux
>> 75724 Paris cedex 15 (FRANCE)
>>
>> Tel: +33 (0)1 45 68 87 01
>> Fax: +33 (0)1 40 61 33 30
>>
>> http://www.bioimageanalysis.org/
>>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
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