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.
The CZI images have a Z-dimension. The planes in the Z-dimension have to be converted into one plane. This can be done by selecting one plane, either fixed in config or dynamically using a focus metric. Another option is to fuse the planes with focus stacking.
[x] Selecting a fixed plane with a config entry
[x] Dynamically selecting a plane per instance using a focus metric
The CZI images have a Z-dimension. The planes in the Z-dimension have to be converted into one plane. This can be done by selecting one plane, either fixed in config or dynamically using a focus metric. Another option is to fuse the planes with focus stacking.