A collection of image processing routines.

git clone https://github.com/fmi-basel/improc.git
pip install improc/

This package consist of a collection of somewhat common functions that are not directly available in libraries such in scikit-image or opencv. That includes (non-exhaustive):

The io sub-module provides a tool to parse a collection of files following the python string formatting syntax and saves the result in a pandas DataFrame. An accessor is also provided to expand pandas with read/write shortcuts for images and csv files. see parse_collection.ipynb for more details.

label and morphology sub-modules contain routines to clean up segmentation labels (filter size, fill-holes, edge smoothing, etc.)

see mesh sub-module

see segmentation sub-module

The regionprops sub-module extends scikit-images' regionprop to multi-channel, multi-label data in a modular way.

see resample sub-module

The czi_reader sub-module provides draft utility functions to read multi-scene czi files. If working prefere using czifile or more actively developed aicspylibczi. (both attempt to create a giant image containing all the scenes and run out of memory)