search

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
7 stars 0 forks source link

Use CellProfiler to extract features #16

Closed MaximLippeveld closed 3 years ago

MaximLippeveld commented 3 years ago

CellProfiler is a software tool for cell profiling that is widely used in the community.

It has a python API, which can be used to construct and run pipelines programmatically. Their wiki includes a good example of how to use cellprofiler as a package.

If we can run this package distributed within Dask, the amount of features we can compute increases a lot.

MaximLippeveld commented 3 years ago

See this gist for an example of computing cellprofiler modules.