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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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Support for other microscopy formats through Bio-Formats #15

Closed MaximLippeveld closed 2 years ago

MaximLippeveld commented 3 years ago

Bio-Formats is a library for writing microscopy image data. It supports many different (proprietary) formats. If we can use Bio-Formats for our data loading, our tool becomes applicable to many more datasets.

Bio-Formats can be used from python with (A) the python-bioformats package or (B) through ImageJ with the pyimagej package.

Given this discussion on the image.sc forum it is not clear what the future is for option (A), so (B) is likely the best option to explore first.

MaximLippeveld commented 3 years ago

First implementation for loading images from CIF-files: https://gist.github.com/MaximLippeveld/a9b3c1472192986ede21879ba0b0dcb8

MaximLippeveld commented 2 years ago

This is currently to difficult because of the Java dependency.