Remove cell table batching functionality

[alex-l-kong]

What is the purpose of this PR?

Addresses stage 1 of #720, removing batching of generate_cell_table.

How did you implement your changes

The batch loop inside generate_cell_table has been changed to a per-FOV iteration.

The call in 1_Segment_Image_Data.ipynb needed to be updated accordingly.

Remaining issues

In particular, changes were made to the way fovs and filenames were being handled in generate_cell_table. MIBItiff support requires us to retrieve filenames, however for non-MIBItiffs the loop needs to be more fully guarded against filenames being set to None (which happens when you call list_files on a folder structure).

We will not have to worry about this once MIBItiff support gets phased out.

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[alex-l-kong]

@benoberlton this PR should address the error caused by variable image sizes you were getting during generate_cell_table. Let me know if any issues pop up.

[alex-l-kong]

@ngreenwald realized I needed to update the documentation for create_marker_count_matrices to indicate that the FOV dimensions should support just a single FOV, however seems I can't push the change until you review the rest of the changes (even if I remove the review request). If all looks good I'll push that change separately.

[ngreenwald]

Huh that's strange, I didn't know review status could block subsequent changes. Won't have time to look tonight, I'll submit this which will hopefully address the issue

[ngreenwald]

Looks good, just need to add back in the code that was removed. Seems like this has happened a bunch of times on your PRs, I think you said your editor does it automatically?

[alex-l-kong]

Looks good, just need to add back in the code that was removed. Seems like this has happened a bunch of times on your PRs, I think you said your editor does it automatically?

@ngreenwald yeah, looks like I'll need to officially need to retire my merge tool lol, Sublime Merge hasn't been the easiest to interface with.

[alex-l-kong]

@ngreenwald this should resolve generate_cell_table with main.