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• Repositories 317
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• Stars 239
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• Overview
• Repositories 317
• Projects 1
• Packages 0
• Stars 239
• Sponsoring 0

tlambert03 (Talley Lambert) · GitHub

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

1. The Fluorescent Protein Database

   Python 70 6

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

   Python 66 18

3. native Python dataclasses for the OME data model

   Python 60 9

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

   Python 67 12

5. Scientific colormaps for python, with only numpy dependency

   Python 127 10

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

   C++ 49 11

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