Give me a starting nudge: microscopy image processing in python

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  • GitHub repo python-bioformats

    Read and write life sciences file formats

    For domain-specific stuff like data formats, look for bindings to libraries used in that domain, which may not be native to Python. From a quick Google, this project may be useful: https://github.com/CellProfiler/python-bioformats/ Unlike say numpy, it may be a road less traveled.

  • GitHub repo ITK

    Insight Toolkit (ITK) -- Official Repository. ITK builds on a proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.

    VTK is a powerful visualization package, but it's more for working with 3D FEM/CFD data. There are lots of things in there though, so it may be useful. The sister project Paraview is an application which can be used to work with data interactively. Both have great Python support. There is also ITK which is focused on with image data, like medical scans - never used it, though.

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  • GitHub repo aicsimageio

    Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python

    czi: https://github.com/allencellmodeling/aicsimageio nd2: https://rbnvrw.github.io/nd2reader/

NOTE: The number of mentions on this list indicates mentions on common posts plus user suggested alternatives. Hence, a higher number means a more popular project.

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