Was using paquo to directly import results of image processing and cellpose segmentation in python. Realised I needed PathCellObjects like #110
Added QuPathPathCellObject similar to how QuPath{Detection/Tile}Object were implemented. Followed class hierarchy defined in original qupath javadocs.
Added add_cell method to QuPathPathObjectHierarchy
Currently, I have added the parameter defining a secondary roi for the nuclear region as a keyword argument, named nucleus_roi, to not ruin from_shapely for the other pathobject constructors. The first roi, 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) or nucleus_roi.within(roi) to ensure the nuclear polygon given is within the cell.
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.