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.
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.
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 thepyimagej
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.