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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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Dimensionality reduction after feature extraction #19

Closed MaximLippeveld closed 3 years ago

MaximLippeveld commented 3 years ago

Apply UMAP dimensionality reduction using the umap-learn library. Try running first with default parameters. Later we can tweak the most important parameters.

Distributed UMAP is not possible. First convert Dask dataframe to pandas using compute, and then apply UMAP.

sanderthierens commented 3 years ago

Done, plot is in quality report