Software

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)

Other

• napping, an interactive tool for control point mapping and coordinate transformation
• TissUUmaps-schema: pydantic schema for TissUUmaps