angelolab / ark-analysis / 6483

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Rework mask saving and cell labeling to support just single FOV parameter (#737)

* Rework save_fov_images and label_cells_by_cluster

* Fix type hint to pd.DataFrame

* Explicitly import pandas into data_utils

* Fix xarray import

* Fix progress bar update

* Fix neighborhood mask docstring

* Remove redundant comment

* Change neighborhood mask generation function to match signature of other mask generation functions

* Add test for neighborhood mask function

* Nuke cluster_labels_xr to neighborhood_masks

* Make sure all FOVs are visualized at the end of the neighborhood notebook

* Change save_fov_image to save_fov_mask, and update dtypes to ensure int16 automatically gets passed in

* Make sure Mantis project creation works with renamed mask generation function

* Clarify documentation of save_fov_mask

41 of 41 new or added lines in 2 files covered. (100.0%)

2966 of 3136 relevant lines covered (94.58%)

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