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InCell: allow mix of 2D and 3D channels to be treated as a Z stack #4270

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See https://forum.image.sc/t/incell-plates-with-z-stacks-cannot-be-imported-on-omero/107802 and data copied to inbox/imagesc-107802.

As indicated in the forum post, one channel in the plate has a Z stack (16 slices), while the remaining channels have a single Z slice. The changes in lines 795 and later are to pick up the dimensions of each field as 16 Z x 4 C, with most planes blank.

The changes in lines 467-468 are necessary because the total image count is 152, and the number of planes per field is 64 - so the expectedSeries calculation results in 2, when there are actually 8 series (4 fields x 2 wells). This change in particular might break some older data, so we'll see what the test results are, and may need to exclude/rework this a bit.

Adding to 8.1.1 milestone instead of 8.1.0, anticipating that some extra work will be needed.

@melissalinkert melissalinkert added this to the 8.1.1 milestone Jan 28, 2025
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This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/incell-plates-with-z-stacks-cannot-be-imported-on-omero/107802/2

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jburel commented Jan 29, 2025

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