BodenmillerGroup

ImcSegmentationPipeline

A pixel classification based multiplexed image segmentation pipeline

steinbock

A toolkit for processing multiplexed tissue images

cytomapper

R package for visualization of highly multiplexed imaging data

xtiff

A tiny Python library for writing multi-channel TIFF stacks.

IMCDataAnalysis

R based workflow for multiplexed imaging data

imcRtools

An R package for handling and analysing imaging mass cytometry data

readimc

Python package for reading imaging mass cytometry (IMC) files

napari-imc

Imaging Mass Cytometry (IMC) file type support for napari

histocat-web

Histology Topography Cytometry Analysis Toolbox (histoCAT) for Web.

cytoviewer

An interactive multi-channel image viewer for R

demos

Repository containing demonstrations of lab software

imcdatasets

ExperimentHub collection of imaging mass cytometry datasets

napari-czifile2

Carl Zeiss Image (.czi) file support for napari

napari-roi

Select regions of interest (ROIs) using napari

napari-hierarchical

Complex bio-image file format support for napari

BC_LN_metastses

mcd2zarr

Command line tool to convert MCD files to Zarr

napping

Control point mapping and coordinate transformation using napari

CellSighter

Code for the use of CellSighter in the Bodenmiller Lab

histoCAT

Histology Topography Cytometry Analysis Toolbox

IMC_NSCLC_CAF

IMC analyis CAFs in NSCLC

MEZ_XRF

This is the repository companion to the MEZ-XRF paper

napari-networkx

A napari plugin to read and write spatial graphs using networkx

SABER-IMC_publication

TestData

A central repository to store small datasets for testing purposes

.github

CISI-IMC_publication

Scripts for CISI-IMC publication

napari-labels2graph

A napari plugin to create spatial graphs from labels layers

sp2rd

R package to generate animated transitions between spatial locations and reduced dimensional embeddings

TNBC_publication

Code repository - TNBC IMC study