This organization serves the purpose to collect analysis and software repositories associated to our research.
General instructions on how to analyse imaging mass cytometry (IMC) data can be found in the IMC data analysis workflow. For general discussions and questions relating to IMC data analysis, please raise an issue here.
The following tools have been developed by the lab to perform multiplexed image analysis:
- steinbock for containerized image processing and segmentation.
- readimc for reading raw IMC data.
- ImcSegmentationPipeline for interactive IMC data processing and segmentation.
- napari-imc for interactive visualization of IMC raw data in napari.
- cytomapper for multiplexed image visualization in R.
- cytoviewer for interactive multiplexed image visualization in R.
- imcRtools for single-cell and spatial analysis in R.
- IMCDataAnalysis for a reproducible workflow on multiplexed image downstream analysis in R.
- imcdatasets for a collection of publicly available IMC datasets in R.
Please open issues in the relevant repositories to file bug reports or feature requests.