BodenmillerGroup

Pinned Repositories

cytomapper
R package for visualization of highly multiplexed imaging data
Language:R32 10 698
cytoviewer
An interactive multi-channel image viewer for R
Language:R5 5 71
IMCDataAnalysis
R based workflow for multiplexed imaging data
Language:HTML28 9 6911
imcRtools
An R package for handling and analysing imaging mass cytometry data
Language:R20 14 759
ImcSegmentationPipeline
A pixel classification based multiplexed image segmentation pipeline
Language:Jupyter Notebook83 22 11535
imctools
Tools to handle IMC data
Language:Python22 21 8315
readimc
Python package for reading imaging mass cytometry (IMC) files
Language:Python12 6 76
SCPathology_publication
The Single-Cell Pathology Landscape of Breast Cancer
Language:MATLAB21 8 57
steinbock
A toolkit for processing multiplexed tissue images
Language:Python49 10 20714
xtiff
A tiny Python library for writing multi-channel TIFF stacks.
Language:Python27 6 122

BodenmillerGroup's Repositories

BodenmillerGroup/ImcSegmentationPipeline
A pixel classification based multiplexed image segmentation pipeline
Language:Jupyter Notebook83 22 11535
BodenmillerGroup/steinbock
A toolkit for processing multiplexed tissue images
Language:Python49 10 20714
BodenmillerGroup/cytomapper
R package for visualization of highly multiplexed imaging data
Language:R32 10 698
BodenmillerGroup/IMCDataAnalysis
R based workflow for multiplexed imaging data
Language:HTML28 9 6911
BodenmillerGroup/xtiff
A tiny Python library for writing multi-channel TIFF stacks.
Language:Python27 6 122
BodenmillerGroup/imcRtools
An R package for handling and analysing imaging mass cytometry data
Language:R20 14 759
BodenmillerGroup/readimc
Python package for reading imaging mass cytometry (IMC) files
Language:Python12 6 76
BodenmillerGroup/napari-imc
Imaging Mass Cytometry (IMC) file type support for napari
Language:Python9 5 302
BodenmillerGroup/histocat-web
Histology Topography Cytometry Analysis Toolbox (histoCAT) for Web.
Language:Vue8 4 2211
BodenmillerGroup/cytoviewer
An interactive multi-channel image viewer for R
Language:R5 5 71
BodenmillerGroup/demos
Repository containing demonstrations of lab software
5 6 01
BodenmillerGroup/imcdatasets
ExperimentHub collection of imaging mass cytometry datasets
Language:R5 5 143
BodenmillerGroup/napari-czifile2
Carl Zeiss Image (.czi) file support for napari
Language:Python5 4 54
BodenmillerGroup/napari-roi
Select regions of interest (ROIs) using napari
Language:Python4 6 71
BodenmillerGroup/BC_LN_metastses
Language:Jupyter Notebook2 4 00
BodenmillerGroup/IMC_NSCLC_CAF
IMC analyis CAFs in NSCLC
2 4 1
BodenmillerGroup/mcd2zarr
Command line tool to convert MCD files to Zarr
Language:Python2 4 2
BodenmillerGroup/napping
Control point mapping and coordinate transformation using napari
Language:Python2 5 200
BodenmillerGroup/CellSighter
Code for the use of CellSighter in the Bodenmiller Lab
Language:R1 0 0
BodenmillerGroup/histoCAT
Histology Topography Cytometry Analysis Toolbox
Language:MATLAB1 0 02
BodenmillerGroup/MEZ_XRF
This is the repository companion to the MEZ-XRF paper
Language:Jupyter Notebook1 1 00
BodenmillerGroup/napari-networkx
A napari plugin to read and write spatial graphs using networkx
Language:Python1 5 01
BodenmillerGroup/SABER-IMC_publication
1 5 0
BodenmillerGroup/TestData
A central repository to store small datasets for testing purposes
Language:Shell1 16 55
BodenmillerGroup/.github
5 01
BodenmillerGroup/BCmet_publication_scripts
Language:R
BodenmillerGroup/CISI-IMC_publication
Scripts for CISI-IMC publication
Language:Jupyter Notebook5 0
BodenmillerGroup/MelanomaIMC
check static webpage here:
Language:R1
BodenmillerGroup/napari-labels2graph
A napari plugin to create spatial graphs from labels layers
Language:Python1
BodenmillerGroup/TNBC_publication
Code repository - TNBC IMC study
Language:Jupyter Notebook