Pinned Repositories
cytomapper
R package for visualization of highly multiplexed imaging data
cytoviewer
An interactive multi-channel image viewer for R
IMCDataAnalysis
R based workflow for multiplexed imaging data
imcRtools
An R package for handling and analysing imaging mass cytometry data
ImcSegmentationPipeline
A pixel classification based multiplexed image segmentation pipeline
imctools
Tools to handle IMC data
readimc
Python package for reading imaging mass cytometry (IMC) files
SCPathology_publication
The Single-Cell Pathology Landscape of Breast Cancer
steinbock
A toolkit for processing multiplexed tissue images
xtiff
A tiny Python library for writing multi-channel TIFF stacks.
BodenmillerGroup's Repositories
BodenmillerGroup/ImcSegmentationPipeline
A pixel classification based multiplexed image segmentation pipeline
BodenmillerGroup/steinbock
A toolkit for processing multiplexed tissue images
BodenmillerGroup/cytomapper
R package for visualization of highly multiplexed imaging data
BodenmillerGroup/IMCDataAnalysis
R based workflow for multiplexed imaging data
BodenmillerGroup/xtiff
A tiny Python library for writing multi-channel TIFF stacks.
BodenmillerGroup/imcRtools
An R package for handling and analysing imaging mass cytometry data
BodenmillerGroup/readimc
Python package for reading imaging mass cytometry (IMC) files
BodenmillerGroup/napari-imc
Imaging Mass Cytometry (IMC) file type support for napari
BodenmillerGroup/histocat-web
Histology Topography Cytometry Analysis Toolbox (histoCAT) for Web.
BodenmillerGroup/cytoviewer
An interactive multi-channel image viewer for R
BodenmillerGroup/demos
Repository containing demonstrations of lab software
BodenmillerGroup/imcdatasets
ExperimentHub collection of imaging mass cytometry datasets
BodenmillerGroup/napari-czifile2
Carl Zeiss Image (.czi) file support for napari
BodenmillerGroup/napari-roi
Select regions of interest (ROIs) using napari
BodenmillerGroup/BC_LN_metastses
BodenmillerGroup/IMC_NSCLC_CAF
IMC analyis CAFs in NSCLC
BodenmillerGroup/mcd2zarr
Command line tool to convert MCD files to Zarr
BodenmillerGroup/napping
Control point mapping and coordinate transformation using napari
BodenmillerGroup/CellSighter
Code for the use of CellSighter in the Bodenmiller Lab
BodenmillerGroup/histoCAT
Histology Topography Cytometry Analysis Toolbox
BodenmillerGroup/MEZ_XRF
This is the repository companion to the MEZ-XRF paper
BodenmillerGroup/napari-networkx
A napari plugin to read and write spatial graphs using networkx
BodenmillerGroup/SABER-IMC_publication
BodenmillerGroup/TestData
A central repository to store small datasets for testing purposes
BodenmillerGroup/.github
BodenmillerGroup/BCmet_publication_scripts
BodenmillerGroup/CISI-IMC_publication
Scripts for CISI-IMC publication
BodenmillerGroup/MelanomaIMC
check static webpage here:
BodenmillerGroup/napari-labels2graph
A napari plugin to create spatial graphs from labels layers
BodenmillerGroup/TNBC_publication
Code repository - TNBC IMC study