[ome-users] bio-formats problem reading ND2 files with several stage positions

[Ponti Aaron]

Hi,

we have ND2 files that contain several stage (XY) positions. At every stage position, a few stacks of a few tens of planes over a few channels and a few time points are acquired.

Bio-Formats (5.0.0) seems to get all dimensions correctly, but then it misinterprets the sequences of planes and redistributes them over the wrong axes.

Specifically, even though the number of series in the file match the number of stage positions, the T, C, and Z dimensions match the ones in each series, when you look at the opened stacks you see that it contains segments from different stage positions. Swapping dimensions while opening does not help, because you can do it for planes within a series; here the problem is that the planes are read "horizontally" over stage positions.

I have a good example file if you would like to have it (a.k.a. where can I upload it ;-) ?)

Thanks a lot in advance
a2

----
Dr. Aaron Ponti
Software and Data Management Engineer
Single Cell Unit
Department of Biosystems Science and Engineering (D-BSSE)
ETH Zürich
Office 2.24
Mattenstrasse 26
4058 Basel, Switzerland
aaron.ponti at bsse.ethz.ch
+41 61 387 33 74

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