angelolab / ark-analysis / 8058209876

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1100 empty composites masks in ez segmenter notebook (#1101)

* Added fixes for  issue where float TIFFs were being converted to int and compromising downstream composite, segmentation pipeline.

* Added float conversion for composite_array.

* Fixed composite array dtype issue where original array was being overwritten during composite creation.

* Fixed composite array creation issue - couldn't add np arrays using +=

* added image scaling fix for displaying channels

* Updated tests to accomodate new dtype np.float32 in composite array, channel_display formats.

* Added marker_quantification.process_lists() search function.

* Fixed issue with display_channel (trashed ubyte).

* Fixed issue with display_channel (trashed ubyte).

* Changes merging functions so any cell name can serve as cell type, no longer is whole_cell enforced.

* Fixed issue with composite overlay display in mask overlay display function.

* merge_masks was calling the incorrect version of label. Now updated to call correct skimage.morphology version.

* updated correct label with correct parameters

* Updated merge_masks_tests.

* Fixed updated variable name in ez template.

* Fixed a couple naming issues.

* Removed uneeded code.

* Sri helped fix the broken merge_masks_se_test.

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Co-authored-by: Sricharan Reddy Varra <srivarra@stanford.edu>

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