Maximum Intensity Projection of segmented clump of cells
3D segmented image: ddf34988-03d5-4fad-98d5-ef74b704a66a.tif (574.6 KB)
Original 3D image: ddf34988-03d5-4fad-98d5-ef74b704a66a.tif (1.5 MB)
I’m trying to segment cells from this 3D microscopic image, via
skimage.filters.apply_hysteresis_threshold but I get this clump instead due to close proximity of the cells.
- My goal is not to compromise any branching information of the cells and still get single segmented cells.
- I’ve tried increasing the thresholds but it compromises a lot of branching of cells which I don’t favor.
- I’ve thought of applying edge filter and then using it as bounds of the branches of single cells, but the edge filters also don’t capture the thin branches well and compromise a lot of detail.
- Bottom part of image might be connected due to blood vessel being an artifact, but the above 2 cells are of good quality and are what I hope to extract.
- I need suggestion for maybe some post-processing technique to dissociate these cells from the clump to achieve my goal