Pinned Repositories
cytomapper
R package for visualization of highly multiplexed imaging data
cytoviewer
An interactive multi-channel image viewer for R
IMCDataAnalysis
R based workflow for multiplexed imaging data
imcRtools
An R package for handling and analysing imaging mass cytometry data
ImcSegmentationPipeline
A pixel classification based multiplexed image segmentation pipeline
imctools
Tools to handle IMC data
readimc
Python package for reading imaging mass cytometry (IMC) files
SCPathology_publication
The Single-Cell Pathology Landscape of Breast Cancer
steinbock
A toolkit for processing multiplexed tissue images
xtiff
A tiny Python library for writing multi-channel TIFF stacks.
BodenmillerGroup's Repositories
BodenmillerGroup/ImcPluginsCP
CellProfiler plugins for multiplexed image analysis
BodenmillerGroup/MISegmentation
Analyzing the performance of the ImcSegmentationPipeline
BodenmillerGroup/cytomapper_publication
See static website at https://bodenmillergroup.github.io/cytomapper_publication/
BodenmillerGroup/SpheroidPublication
This contains the workflows to reproduce all analyses from the Spheroid paper.
BodenmillerGroup/pycytools
BodenmillerGroup/snakemake
This is the development home of the workflow management system Snakemake. For general information, see
BodenmillerGroup/core
BodenmillerGroup/CellProfiler
An open-source application for biological image analysis
BodenmillerGroup/spherpro
Code used for analysis of tumor spheroid data.
BodenmillerGroup/CATALYST
Cytometry dATa anALYsis Tools
BodenmillerGroup/cookiecutter-jupyter
Bodenmiller Lab template for Python data analysis projects using Jupyter notebooks
BodenmillerGroup/bbRtools
R tools for the Bodenmiller lab
BodenmillerGroup/svca
BodenmillerGroup/SCPathology_publication
The Single-Cell Pathology Landscape of Breast Cancer
BodenmillerGroup/imcyto
UNDER CONSTRUCTION: Image Mass Cytometry analysis pipeline
BodenmillerGroup/dockers
collection of Dockerfiles for building docker images
BodenmillerGroup/Rphenograph
Rphenograph: R implementation of the PhenoGraph algorithm
BodenmillerGroup/mcdlib
MCD file parser library
BodenmillerGroup/bbwidgets
Interactive Widgets for the Jupyter Notebook
BodenmillerGroup/ansible-pgserver
The ansible playbook defining the postgres server used for vitoz sphere project.
BodenmillerGroup/HistoSlider
HistoSlider project
BodenmillerGroup/ilastik
ilastik-shell, applets, and workflows to string them together.
BodenmillerGroup/git-training
Git introduction
BodenmillerGroup/ansible-bbclient
Contains the ansible scripts to setup a bbclient
BodenmillerGroup/cytofkit
cytofkit: an integrated flow/mass cytometry data analysis pipeline
BodenmillerGroup/Adnet
Repository for the analysis of the paper "Influence of node abundance on signaling network state and dynamics analyzed by mass cytometry"
BodenmillerGroup/airlab