BodenmillerGroup

Repositories

• TestData

  A central repository to store small datasets for testing purposes
  MIT 0 0 0 0 Updated Mar 8, 2021

• cytomapper

  Docs at https://bodenmillergroup.github.io/cytomapper/

  spatial-analysis single-cell bioimaging imaging-mass-cytometry
  R 3 8 7 0 Updated Mar 7, 2021

• napari-imc

  Imaging Mass Cytometry (IMC) file type support for napari
  Python MIT 0 4 2 0 Updated Mar 5, 2021

• napari-czifile2

  Carl Zeiss Image (.czi) file support for napari
  Python MIT 0 1 1 1 Updated Mar 4, 2021

• imctools

  Tools to handle IMC data

  tiff mcd ome-tiff imc imc-data
  Python MIT 10 12 27 0 Updated Mar 3, 2021

• napping

  Control point mapping and coordination transformation using napari
  Python MIT 0 1 3 1 Updated Mar 2, 2021

• histoCAT3D

  Repository for the release version of histoCAT++
  Objective-C AGPL-3.0 0 0 0 0 Updated Feb 25, 2021

• ImcSegmentationPipeline

  A pixelclassification based multiplexed image segmentation pipeline

  pipeline ubuntu cellprofiler segmentation imc pixel-classification
  Jupyter Notebook MIT 13 30 15 3 Updated Feb 25, 2021

• ImcSegmentationSnakemake

  The repository for the Snakemake implementation of the ImcSegmentationPipeline
  Python MIT 0 2 2 0 Updated Feb 18, 2021

• ImcPluginsCP

  CellProfiler plugins for multiplexed image analysis
  Python 6 7 0 1 Updated Feb 16, 2021

• imcdatasets

  ExperimentHub collection of imaging mass cytometry datasets
  R 0 1 3 0 Updated Feb 2, 2021

• xtiff

  A small Python 3 library for writing multi-channel TIFF stacks
  Python MIT 0 5 1 0 Updated Jan 20, 2021

• MISegmentation

  Analyzing the performance of the ImcSegmentationPipeline
  Jupyter Notebook MIT 0 0 0 0 Updated Jan 11, 2021

• cytomapper_publication

  See static website at https://bodenmillergroup.github.io/cytomapper_publication/
  R MIT 1 1 0 0 Updated Jan 11, 2021

• SpheroidPublication

  This contains the workflows to reproduce all analyses from the Spheroid paper.
  Makefile MIT 0 1 0 0 Updated Jan 1, 2021

• pycytools
  Python BSD-3-Clause 0 0 1 0 Updated Dec 23, 2020

• snakemake

  Forked from snakemake/snakemake

  This is the development home of the workflow management system Snakemake. For general information, see
  HTML MIT 196 0 0 0 Updated Dec 22, 2020

• neighbouRhood

  Adds an R implementation for the HistoCAT neightbourhood analysis that runs from CellProfiler output.
  R LGPL-3.0 4 1 3 0 Updated Dec 2, 2020

• core

  Forked from CellProfiler/core
  Python 8 0 0 0 Updated Nov 17, 2020

• CellProfiler

  Forked from CellProfiler/CellProfiler

  An open-source application for biological image analysis
  Python 273 0 0 0 Updated Oct 23, 2020

• cyTOFcompensation

  Companion repository for the paper 'Compensation of signal spillover in suspension and imaging mass cytometry'
  HTML MIT 6 4 1 1 Updated Oct 23, 2020

• spherpro

  Code used for analysis of tumor spheroid data.
  Python BSD-3-Clause 0 1 26 0 Updated Sep 28, 2020

• bbsnippets

  This repository contains general examples, code snippets and guidelines.

  smc cytometry imc
  HTML 0 0 3 4 Updated Sep 25, 2020

• histoCAT

  Histology Topography Cytometry Analysis Toolbox
  MATLAB 16 36 24 (1 issue needs help) 0 Updated Sep 4, 2020

• IntroDataAnalysis

  Repository for teaching and instruction purposes
  Jupyter Notebook 1 8 0 0 Updated Jun 3, 2020

• cookiecutter-jupyter

  Bodenmiller Lab template for Python data analysis projects using Jupyter notebooks
  Jupyter Notebook MIT 0 1 0 0 Updated May 15, 2020

• bbRtools

  R tools for the Bodenmiller lab
  R LGPL-3.0 2 0 10 0 Updated May 13, 2020

• svca

  Forked from damienArnol/svca
  C++ Apache-2.0 7 0 0 0 Updated Mar 13, 2020

• SCPathology_publication

  The Single-Cell Pathology Landscape of Breast Cancer
  MATLAB MIT 4 6 0 0 Updated Jan 14, 2020

• imcyto

  Forked from nf-core/imcyto

  UNDER CONSTRUCTION: Image Mass Cytometry analysis pipeline
  Python MIT 8 0 0 0 Updated Dec 17, 2019