You can find further software on my GitHub profile.

Multiplexed tissue imaging

  • readimc, a Python package for reading Imaging Mass Cytometry (IMC) data
  • steinbock, a dockerized multi-channel image processing toolkit
  • spellmatch, a command-line tool for spatial cell representation matching (discontinued)
  • xtiff, a tifffile wrapper for writing multi-channel image stacks (legacy)
  • imdlib, a library for reading CyTOF .imd files in C++/Python (archived)
  • biobrowse, an ImageJ plugin for browsing multi-channel images (access upon request)

napari plugins

  • napari-czifile2: load Carl Zeiss Image (.czi) files
  • napari-roi: choose and export regions of interest (ROIs)
  • napari-imc: load and visualize Imaging Mass Cytometry (IMC) data
  • napari-hierarchical: generalization of napari-imc to other container formats (e.g. HDF5, Zarr, netCDF4; under development)
  • napari-labels2graph: create spatial graphs from labels layers (under development)
  • napari-networkx: read and write spatial graphs using networkx (under development)