BodenmillerGroup
Pinned repositories
Repositories
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TestData
A central repository to store small datasets for testing purposes
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napari-imc
Imaging Mass Cytometry (IMC) file type support for napari
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napari-czifile2
Carl Zeiss Image (.czi) file support for napari
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napping
Control point mapping and coordination transformation using napari
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histoCAT3D
Repository for the release version of histoCAT++
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ImcSegmentationPipeline
A pixelclassification based multiplexed image segmentation pipeline
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ImcSegmentationSnakemake
The repository for the Snakemake implementation of the ImcSegmentationPipeline
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ImcPluginsCP
CellProfiler plugins for multiplexed image analysis
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imcdatasets
ExperimentHub collection of imaging mass cytometry datasets
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xtiff
A small Python 3 library for writing multi-channel TIFF stacks
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MISegmentation
Analyzing the performance of the ImcSegmentationPipeline
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cytomapper_publication
See static website at https://bodenmillergroup.github.io/cytomapper_publication/
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SpheroidPublication
This contains the workflows to reproduce all analyses from the Spheroid paper.
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snakemake
Forked from snakemake/snakemakeThis is the development home of the workflow management system Snakemake. For general information, see
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neighbouRhood
Adds an R implementation for the HistoCAT neightbourhood analysis that runs from CellProfiler output.
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core
Forked from CellProfiler/core -
CellProfiler
Forked from CellProfiler/CellProfilerAn open-source application for biological image analysis
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cyTOFcompensation
Companion repository for the paper 'Compensation of signal spillover in suspension and imaging mass cytometry'
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spherpro
Code used for analysis of tumor spheroid data.
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bbsnippets
This repository contains general examples, code snippets and guidelines.
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histoCAT
Histology Topography Cytometry Analysis Toolbox
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IntroDataAnalysis
Repository for teaching and instruction purposes
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cookiecutter-jupyter
Bodenmiller Lab template for Python data analysis projects using Jupyter notebooks
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bbRtools
R tools for the Bodenmiller lab
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svca
Forked from damienArnol/svca -
SCPathology_publication
The Single-Cell Pathology Landscape of Breast Cancer
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