Bio-Formats mixing up multi-position and time in ND2 file created with JOBS module

Hi all,

I don’t know if this is a widespread problem with ND2 files or just those created with the NIS-Elements JOBS module (http://www.nis-elements.cz/en/solutions/jobs/27) but I have a file someone has collected using this module which was set up to capture three channels from 5 fields of view in each of 8 wells for 89 time points.

The resultant ND2 file should have 40 positions of 89 slices each (plus the 3 channels). When opening in FIJI (Bio-Formats 6.0.1) it gives a list of 40 series all with 89 times format so seems correct but when you open a series there seems to be no time continuity. Upon further investigation, it’s clear that it’s mixing up the series and timepoints such that the below pattern fits.

NIS S 1 - T 1 is Bio-Formats S 1 - T 1
NIS S 1 - T 2 is Bio-Formats S 2 - T 1
NIS S 1 - T 40 is Bio-Formats S 40 - T 1
NIS S 1 - T 41 is Bio-Formats S 2 - T 2
NIS S 1 - T 80 is Bio-Formats S 2 - T 40
NIS S 1 – T 89 is Bio-Formats S 3 – T 9
NIS S 2 – T 1 is Bio-Formats S 3 – T 10

I searched open issues on GIthub but didn’t find anyone else reporting this issue.

Hi @lmurphy, thank you for reporting the issue. This looks as though it is likely the same issue as we have seen previous reports for (https://trello.com/c/LEjj3O3A/281-nd2-timepoints-incorrectly-detected-as-series). If you have any additional sample files which we can use for testing you can upload them to https://www.openmicroscopy.org/qa2/qa/upload/