[ome-users] Bio-Formats ND2 importer bug

[David Gault (Staff)]

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/

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