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@vispy @conda-forge @funkelab @scopetools @pymmcore-plus @pyapp-kit
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I'm a neurobiologist and microscopist by training, and I enjoy maintaining libraries in the general ecosystem of python image visualization and analysis.

  • I was a core developer of napari.
  • Many of the reusable patterns I developed there have been extracted into reusable libraries in the pyapp-kit organization which I continue to maintain.
  • I also maintain the pymmcore-plus organization, a set of packages for microscopy aquisition in pure-python/C++ environments.

In this github org, notable libraries include:

  • FPbase: source code for, the fluorescent protein database.
  • nd2: modern nd2 (Nikon NIS-elements) file reader with broad support
  • ome-types: Python classes for working with the OME datamodel (i.e. OME-XML metadata)
  • pycudadecon: Python wrapper for CUDA-accelerated 3D deconvolution for microscopy
  • pycudasirecon: CUDA-accelerated reconstruction for 3D-structured-illumination
  • cmap: Comprehensive colormap library, with only numpy dependency
  • PSFmodels: Scalar and vectorial models of the 3D microscope point spread function.
  • mrc: deltavision (.mrc/.dv) image file format reader/writer.

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  1. FPbase FPbase Public

    The Fluorescent Protein Database

    Python 63 5

  2. nd2 nd2 Public

    Full-featured nd2 (Nikon NIS Elements) file reader for python. Outputs to numpy, dask, and xarray. Exhaustive metadata extraction

    Python 49 15

  3. ome-types ome-types Public

    native Python dataclasses for the OME data model

    Python 50 9

  4. pycudadecon pycudadecon Public

    Python wrapper for cudaDecon - GPU accelerated 3D deconvolution for microscopy

    Python 56 12

  5. cmap cmap Public

    Scientific colormaps for python, with only numpy dependency

    Python 61 3

  6. PSFmodels PSFmodels Public

    Python bindings for scalar and vectorial models of the 3D microscope point spread function.

    C++ 40 8