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

[David Gault (Staff)]

Hi Aaron,

Does this issue occur both with and without the chunk map option enabled?

In FIJI you can change the option for ND2 files to use the chunk map table by setting the it as below:
Plugins > Bio-Formats > Bio-Formats Plugins Configuration > Formats > Nikon ND2 > Chunkmap


With Thanks,
David Gault

On 8 Aug 2018, at 12:46, Ponti Aaron <aaron.ponti at bsse.ethz.ch<mailto:aaron.ponti at bsse.ethz.ch>> wrote:

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
----
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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