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