[ome-users] Bioformats 5.9.0 reads ND2 files along the wrong dimensions (series vs. timepoints)

[Ponti Aaron]

Hi, everyone

We recently observed that multi-position, multi-color, time-lapse ND2 files generated by the NIS Elements software (version V5.02.00 build 1266 Patch 03 LO, 64bit) on a Nikon Ti2 microscope are not parsed correctly by bioformats (version 5.9.0 included).

To better explain the issue, let's consider an example dataset we recently acquired: it is a 120-position (series), 16-timepoint, 2-channel, 1-plane dataset. (I would like to upload it, if you can give me the coordinates of your FTP server.)

Bioformats correctly lists 120 series, each with T = 16, C = 2, Z = 1 but when opening series = 1 and going through T = 1 to 16, bioformats incorrectly loads the images corresponding to T = 1 for series 1 through 16 instead (in other words, series and time indices are swapped). This can easily be seen by browsing the dataset in Fiji vs. NIS Elements.

Thanks in advance for looking into it. Please let me know how to provide you with the example dataset (~ 8GB).
a2
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Dr. Aaron Ponti
Software and Data Management Engineer
Image Analysis Specialist
Single Cell Facility
Department of Biosystems Science and Engineering (D-BSSE)
ETH Zürich
Office 2.30
Mattenstrasse 26
4058 Basel, Switzerland
aaron.ponti at bsse.ethz.ch<mailto:aaron.ponti at bsse.ethz.ch>
T: +41 61 387 33 74
F: +41 61 387 39 93

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