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 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 fpbase.org, 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.
- microsim: fluorescence microscopy simulation framework
- mkdocs-api-autonav: API documentation autogeneration for mkdocs