angelolab / ark-analysis / 7038274386 / 1

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ezSegmentation (#958)

* added started ez_seg file + test

* applied filters.threshold_local's output to create a binary mask

* Adding merge_mask functionality to be later built into merge_masks notebook.

* added composite builder functionality - ready for refactoring

* ezseg_v1 notebook

* Second version of ez notebook started, changes to composite builder and mask merging, as well as new within-notebook display functionality found in ez_seg_display.py.

* Added a relabeleing step necessary for masks merging. Need to test it's mask vs channel import setup.

* refactor stage 1

refactor stage 2

* refactoring pt.2

refactor

refactor pt.3

* refactor pt. 3

* added ez_seg folder in tests

* switch order of composite builder & mask creator, added mask_name to mask creator section of notebook

* notebook adjustments

* notebook adjustments v3

* modified:   templates/ez_testing/ezseg_v2.ipynb

* refactor sections 1-3

* removed unused import

* renumber mask adjustments

* Switched ordering of mask merge and mask relabeling. Additionally updated cell table function with appropriate path names. Need to ensure this will loop through entire ez_masks to create a single table.

* Renamed the dir input to cell table creation as root_mask_dir to account for additional sources of masks.

* Composite builder now iterates over all input fov's. Bug fixed where add & subtract weren't working due to array type of uint8 (changed to int).

* Fixed problem with ez segmentation mask maker not performing size exclusion properly due to lack of boolean screen. Additionally re-wrote mask saving.

* Updated visuals for composite, mask overlay. Updated notebook with multiple different input parameters for seg. Fixed issue with segmentation process where import of a folder with one tiff could not be read into _create_object_masks.

* Updated display code and notebook cells for ez segmentation step.

* Updated ez segmentation, merging, and mask display functions.

* Fixed re... (continued)

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