BodenmillerGroup

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88 repositories

readimc
Public
Python package for reading imaging mass cytometry (IMC) files
Python
•
MIT License
•7•13•4•1•Updated Jan 13, 2025Jan 13, 2025
steinbock
Public
A toolkit for processing multiplexed tissue images
Python
•
MIT License
•17•53•31•3•Updated Jan 6, 2025Jan 6, 2025
xtiff
Public
A tiny Python library for writing multi-channel TIFF stacks.
Python
•
MIT License
•4•28•4•2•Updated Jan 6, 2025Jan 6, 2025
napping
Public
Control point mapping and coordinate transformation using napari
Python
•
MIT License
•1•2•1•1•Updated Jan 6, 2025Jan 6, 2025
napari-roi
Public
Select regions of interest (ROIs) using napari
Python
•
MIT License
•2•4•3•1•Updated Jan 6, 2025Jan 6, 2025
napari-czifile2
Public
Carl Zeiss Image (.czi) file support for napari
Python
•
MIT License
•7•6•0•1•Updated Jan 6, 2025Jan 6, 2025
mcd2zarr
Public
Command line tool to convert MCD files to Zarr
ome-zarr-converter
Python
•
MIT License
•1•2•2•1•Updated Jan 6, 2025Jan 6, 2025
airlab-rs
Public
AirLab backend
Rust
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MIT License
•0•0•2•0•Updated Dec 2, 2024Dec 2, 2024
imcRtools
Public
An R package for handling and analysing imaging mass cytometry data
spatial imc r single-cell
R
•10•22•9•2•Updated Oct 29, 2024Oct 29, 2024
CISI-IMC
Public
Jupyter Notebook
•
MIT License
•0•0•0•0•Updated Oct 13, 2024Oct 13, 2024
TNBC_publication
Public
Code repository - TNBC IMC study
Jupyter Notebook
•0•0•0•0•Updated Sep 5, 2024Sep 5, 2024
BCmet_publication_scripts
Public
R
•1•1•0•0•Updated Aug 29, 2024Aug 29, 2024
cytomapper
Public
R package for visualization of highly multiplexed imaging data
spatial-analysis bioimaging imaging-mass-cytometry single-cell
R
•9•31•9•2•Updated Jun 25, 2024Jun 25, 2024
cytoviewer
Public
An interactive multi-channel image viewer for R
bioconductor imaging visualization r shiny
R
•1•6•0•0•Updated Jun 25, 2024Jun 25, 2024
MelanomaIMC
Public
check static webpage here:
R
•1•0•0•1•Updated May 20, 2024May 20, 2024
imcdatasets
Public
ExperimentHub collection of imaging mass cytometry datasets
R
•
GNU General Public License v3.0
•4•5•4•0•Updated Mar 16, 2024Mar 16, 2024
IMCDataAnalysis
Public
R based workflow for multiplexed imaging data
bioconductor spatial-analysis image-analysis single-cell
HTML
•
MIT License
•12•28•4•1•Updated Feb 12, 2024Feb 12, 2024
.github
Public
0•0•0•0•Updated Jan 29, 2024Jan 29, 2024
CellSighter
Public
Code for the use of CellSighter in the Bodenmiller Lab
R
•7•1•0•0•Updated Dec 19, 2023Dec 19, 2023
IMC_NSCLC_CAF
Public
IMC analyis CAFs in NSCLC
0•2•1•0•Updated Dec 13, 2023Dec 13, 2023
ImcSegmentationPipeline
Public template
A pixel classification based multiplexed image segmentation pipeline
pipeline ubuntu cellprofiler imc pixel-classification segmentation
Jupyter Notebook
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MIT License
•35•85•6•0•Updated Dec 5, 2023Dec 5, 2023
CISI-IMC_publication
Public
Scripts for CISI-IMC publication
Jupyter Notebook
•
MIT License
•0•0•0•0•Updated Nov 29, 2023Nov 29, 2023
napari-imc
Public
Imaging Mass Cytometry (IMC) file type support for napari
Python
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MIT License
•3•9•8•1•Updated Oct 19, 2023Oct 19, 2023
TestData
Public
A central repository to store small datasets for testing purposes
Shell
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Creative Commons Attribution 4.0 International
•5•1•2•0•Updated Sep 26, 2023Sep 26, 2023
demos
Public
Repository containing demonstrations of lab software
demo bioconductor
1•5•0•0•Updated Sep 14, 2023Sep 14, 2023
MEZ_XRF
Public
This is the repository companion to the MEZ-XRF paper
Jupyter Notebook
•0•1•0•0•Updated Aug 31, 2023Aug 31, 2023
histocat-web
Public
Histology Topography Cytometry Analysis Toolbox (histoCAT) for Web.
python bioinformatics vue data-visualization toolbox scientific segmentation single-cell cytometry imc
Vue
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MIT License
•11•7•11•5•Updated Jul 22, 2023Jul 22, 2023
SABER-IMC_publication
Public
MIT License
•0•1•0•0•Updated May 16, 2023May 16, 2023
histoCAT
Public
Histology Topography Cytometry Analysis Toolbox
MATLAB
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Other
•23•1•0•0•Updated Apr 27, 2023Apr 27, 2023
BC_LN_metastses
Public
Jupyter Notebook
•0•2•0•0•Updated Feb 17, 2023Feb 17, 2023