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ScalableCytometryImageProcessing / SCIP

Scalable Cytometry Image Processing (SCIP) is an open-source tool that implements an image processing pipeline on top of Dask, a distributed computing framework written in Python. SCIP performs projection, illumination correction, image segmentation and masking, and feature extraction.
https://scalable-cytometry-image-processing.readthedocs.io/en/latest/
GNU General Public License v3.0
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Implement possibility to refine masks after CellPose segmentation #47

Open MaximLippeveld opened 2 years ago

MaximLippeveld commented 2 years ago

CellPose produces a mask for one channel only. Running CellPose for every channel is too computationally intensive. This can be solved by using CellPose to get a mask that covers the entire cell, and subsequently refining that mask per channel.

MaximLippeveld commented 2 years ago

Refining the mask within the parent patch proved difficult, because very little context is available around the cell. It should be feasible though, so I will revisit this in the future.

Currently it is only possible to generate a new CellPose mask for a second channel. These segment are then assigned to the parent cell based on overlap.