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

[Maximilian Fries]

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

[cid:image002.jpg at 01D2A7B3.643E1320]

--
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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