ND2 timelapse plus Z stack not detected correctly

[melissalinkert]

This issue has been reported by another user in https://forum.image.sc/t/unable-to-open-nikon-nd2-with-bio-formats/38904/5

A sample file is available at https://zenodo.org/record/7439387#.Y9fA9OzP10t which replicates the issue with Bio-Formats 6.11.1. None of the ND2 reader options impact the behaviour.

In the case of this sample file there are expected to be 44 timepoints, when read with Bio-Formats the timepoints are split into series, but even then only 20 series are displayed and the remaining timepoints are dropped.

Originally posted by @dgault in #3313

Splitting from #3313 as this specific file wasn't fixed by #4341, unlike the rest of the data referenced in #3313. In this case, the series count is detected as 20 (it should be 1), the SizeT is 1 (it should be 44), while the SizeZ (3) and SizeC (5) counts are correct. The difference between 20 and 44 suggests that there is some other plane count calculation issue occurring.

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/imagej-bioformats-importer-incorrectly-reading-metadata/115943/11

[melissalinkert]

As referenced in #4344 (comment), https://zenodo.org/records/16921650 has an example of incorrect Z/T counts and incorrect plane ordering across series. I'm not 100% sure if the root cause is the same, but adding to this issue so that both datasets are investigated together in advance of 8.4.0.