BodenmillerGroup/SpheroidPublication

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Created over 4 years ago
Updated almost 4 years ago

BodenmillerGroup/SpheroidPublication

BodenmillerGroup

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This contains the workflows to reproduce all analyses from the Spheroid paper.

ImcSegmentationPipeline

A pixel classification based multiplexed image segmentation pipeline

Jupyter Notebook

steinbock

A toolkit for processing multiplexed tissue images

cytomapper

R package for visualization of highly multiplexed imaging data

xtiff

A tiny Python library for writing multi-channel TIFF stacks.

IMCDataAnalysis

R based workflow for multiplexed imaging data

imctools

Tools to handle IMC data

SCPathology_publication

The Single-Cell Pathology Landscape of Breast Cancer

imcRtools

An R package for handling and analysing imaging mass cytometry data

ImcPluginsCP

CellProfiler plugins for multiplexed image analysis

readimc

Python package for reading imaging mass cytometry (IMC) files

BCexh_scRNAseq

ImagingWorkshop2023

Central repository for the Multiplexed Tissue Imaging Workshop 2023.

napari-imc

Imaging Mass Cytometry (IMC) file type support for napari

IntroDataAnalysis

Repository for teaching and instruction purposes

histocat-web

Histology Topography Cytometry Analysis Toolbox (histoCAT) for Web.

cyTOFcompensation

Companion repository for the paper 'Compensation of signal spillover in suspension and imaging mass cytometry'

neighbouRhood

Adds an R implementation for the HistoCAT neightbourhood analysis that runs from CellProfiler output.

cytoviewer

An interactive multi-channel image viewer for R

3D_IMC_publication

Jupyter Notebook

napari-czifile2

Carl Zeiss Image (.czi) file support for napari

imcdatasets

ExperimentHub collection of imaging mass cytometry datasets

demos

Repository containing demonstrations of lab software

IMCWorkflow

Overview repository on IMC data analysis

ImcSegmentationSnakemake

The repository for the Snakemake implementation of the ImcSegmentationPipeline

napari-roi

Select regions of interest (ROIs) using napari

CAFclassification

napari-hierarchical

Complex bio-image file format support for napari

MI_Sampling_study

Code and scripts used to perform spatial sampling analysis as described in "Optimizing multiplexed imaging experimental design through tissue spatial segregation estimation"

cytomapper_publication

See static website at https://bodenmillergroup.github.io/cytomapper_publication/

napping

Control point mapping and coordinate transformation using napari

cookiecutter-jupyter

Bodenmiller Lab template for Python data analysis projects using Jupyter notebooks

Jupyter Notebook

BC_LN_metastses

Jupyter Notebook

imctoolkit

Python package for processing segmented multi-channel images

mcd2zarr

Command line tool to convert MCD files to Zarr

BCexh_IMC

To test workflowr

Adnet

Repository for the analysis of the paper "Influence of node abundance on signaling network state and dynamics analyzed by mass cytometry"

Jupyter Notebook

mcdlib

MCD file parser library

imdlib

IMD file parser library

CISI_IMC

scripts for Tsuyoshi's CISI_IMC project

MEZ_XRF

This is the repository companion to the MEZ-XRF paper

Jupyter Notebook

napari-networkx

A napari plugin to read and write spatial graphs using networkx

spherpro

Code used for analysis of tumor spheroid data.

SABER-IMC_publication

ImagingDevelopersMeeting2023

Overview repository for the Multiplexed Image

TestData

A central repository to store small datasets for testing purposes

IMC_NSCLC_CAF

IMC analyis CAFs in NSCLC