[ome-users] Bug (?) report Bioformats 5.4 - ND2 multipoint file scrambled

[David Gault (Staff)]

Hi Maximilian,

One test that would be worth carrying out would be to try the import with the new chunk map configuration switched off to see if the import gives a different result.

With the latest release of Bio-Formats there is a configurable option to use the chunk map table to improve performance. This can be configured via a checkbox in the following dialog:
Plugins -> Bio-Fromats -> Bio-Formats Plugins Configuration -> Nikon ND2

Would you be able to confirm if this still results in the same issue?

With Thanks,
David Gault

On 28 Mar 2017, at 11:06, Maximilian Fries <MF474 at MRC-CU.cam.ac.uk<mailto:MF474 at MRC-CU.cam.ac.uk>> wrote:

Dear list,

I have a 60GB .nd2 file generated using NIS runnin a Nikon microscope. It is a multi-point (25 xy positions), multi-channel (4 channels) time lapse (54 time points). When I open it with BioFormats 5.4 as part of Fjii/ImageJ (2.0.0-rc-59/1.51k; Java 1.8.0_66 on Windows 8.1, 64-bit), it shows all 25 xy positions in the importer window, but the stack that opens for a point is actually not from one position, but each time point is from a different position. I presume that xy is treated as t and vice versa.

I have attached a screenshot of the nd2 opened in NIS Elements to illustrate the structure.

I am not sure whether this is an actual bug or user error. If it is the latter, my apologies, but I would still very much appreciate any support.

Many thanks,
Max

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--
Maximilian Fries
PhD student

Venkitaraman Group
MRC Cancer Unit - University of Cambridge
Hutchison/MRC Research Centre
Box 197, Biomedical Campus
Cambridge
United Kingdom
CB2 0XZ

E-Mail: mf474 at mrc-cu.cam.ac.uk<mailto:mf474 at mrc-cu.cam.ac.uk>
+44 (0) 1223 763376 (office)

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