Add PathCellObjects class and add_cell method #112
Merged
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Hello, my first PR here.
Was using paquo to directly import results of image processing and cellpose segmentation in python. Realised I needed PathCellObjects like #110
QuPathPathCellObject
similar to how QuPath{Detection/Tile}Object were implemented. Followed class hierarchy defined in original qupath javadocs.add_cell
method toQuPathPathObjectHierarchy
Currently, I have added the parameter defining a secondary roi for the nuclear region as a keyword argument, named
nucleus_roi
, to not ruinfrom_shapely
for the other pathobject constructors. The firstroi
, should therefore be the outer bounds of the cell (or cytoplasmic polygon).Not sure if we need some sort of checker like
roi.contains(nucleus_roi)
ornucleus_roi.within(roi)
to ensure the nuclear polygon given is within the cell.Happy to further improve code.