Discover BodenmillerGroup/neighbouRhood Open Source project

A toolkit for processing multiplexed tissue images

steinbock

R package for visualization of highly multiplexed imaging data

cytomapper

xtiff

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

R based workflow for multiplexed imaging data

IMCDataAnalysis

imctools

Tools to handle IMC data

The Single-Cell Pathology Landscape of Breast Cancer

SCPathology_publication

MATLAB

imcRtools

An R package for handling and analysing imaging mass cytometry data

ImcPluginsCP

CellProfiler plugins for multiplexed image analysis

Python package for reading imaging mass cytometry (IMC) files

readimc

BCexh_scRNAseq

Central repository for the Multiplexed Tissue Imaging Workshop 2023.

ImagingWorkshop2023

Imaging Mass Cytometry (IMC) file type support for napari

napari-imc

Repository for teaching and instruction purposes

IntroDataAnalysis

Histology Topography Cytometry Analysis Toolbox (histoCAT) for Web.

histocat-web

Vue

cyTOFcompensation

Companion repository for the paper 'Compensation of signal spillover in suspension and imaging mass cytometry'

An interactive multi-channel image viewer for R

cytoviewer

3D_IMC_publication

Carl Zeiss Image (.czi) file support for napari

napari-czifile2

ExperimentHub collection of imaging mass cytometry datasets

imcdatasets

demos

Repository containing demonstrations of lab software

IMCWorkflow

Overview repository on IMC data analysis

ImcSegmentationSnakemake

The repository for the Snakemake implementation of the ImcSegmentationPipeline

Select regions of interest (ROIs) using napari

napari-roi

Complex bio-image file format support for napari

CAFclassification

napari-hierarchical

Code and scripts used to perform spatial sampling analysis as described in "Optimizing multiplexed imaging experimental design through tissue spatial segregation estimation"

MI_Sampling_study

cytomapper_publication

See static website at https://bodenmillergroup.github.io/cytomapper_publication/

napping

Control point mapping and coordinate transformation using napari

Bodenmiller Lab template for Python data analysis projects using Jupyter notebooks

cookiecutter-jupyter

BC_LN_metastses

Python package for processing segmented multi-channel images

imctoolkit

Command line tool to convert MCD files to Zarr

mcd2zarr

Repository for the analysis of the paper "Influence of node abundance on signaling network state and dynamics analyzed by mass cytometry"

BCexh_IMC

To test workflowr

Adnet

This contains the workflows to reproduce all analyses from the Spheroid paper.

SpheroidPublication

Makefile

mcdlib

MCD file parser library

C++

imdlib

IMD file parser library

C++

CISI_IMC

scripts for Tsuyoshi's CISI_IMC project

This is the repository companion to the MEZ-XRF paper

MEZ_XRF

A napari plugin to read and write spatial graphs using networkx

napari-networkx

Code used for analysis of tumor spheroid data.

spherpro