Remove batching functionality from cell and pixel mask generation

[alex-l-kong]

What is the purpose of this PR?

Addresses part 2 of #718.

How did you implement your changes

Change the iteration in generate_and_save_{pixel/cell}_cluster_masks to a per-FOV basis, which requires deprecating the batch_size parameter.

generate_{pixel/cell}_cluster_mask will also support just a single fov string identifying which FOV to process (as opposed to a batch of FOVs).

Because save_fov_images and label_cells_by_cluster are used elsewhere in the repo, it's best to continue requiring a fovs list for these, and instead pass in a list with a single FOV from generate_{pixel/cell}_cluster_mask.

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[ngreenwald]

Which other functions use save_fov_images and label_cells_by_cluster? Are we going to end up removing the batching functionality from them in the future? Or is it really worth keeping them as is?

[alex-l-kong]

@ngreenwald label_cells_by_cluster is called in both the post-clustering notebook (via call to create_mantis_project) and the neighborhood analysis notebook, both of which pass in a list of FOVs. save_fov_images seems just limited to create_mantis_project, which also passes in a list of FOVs.

I thought about looping over each FOV in the create_mantis_project function, but this doesn't resolve the issue in the neighborhood analysis notebook. I have a few ideas about how to condense this to allow save_fov_images and create_mantis_project to work on just single FOVs, however it requires some refactoring to be done in the neighborhood analysis notebook itself. Not sure if this is within the scope of this PR, we can address that in a separate PR if need be.

[ngreenwald]

Okay agreed, that should be a separate PR. As you find stuff like that, go ahead and add it to the overall design doc so we can keep track of what else needs to be changed.