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anndata

Annotated data.

awesome_spatial_omics

tools and notes for spatial omics

card

cellpose

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

cellprofiler

An open-source application for biological image analysis

cellprofiler-analyst

Open-source software for exploring and analyzing large, high-dimensional image-derived data.

cellprofiler-plugins

Community-contributed and experimental CellProfiler modules.

clustergrammer2-notebooks

Examples using Clustergrammer2 to explore high-dimensional datasets.

colocalisation_analysis

Fiji's plugin for colocalization analysis

core

Core classes and components used by CellProfiler

csv-to-fcs

A short script for converting .csv file data into an .fcs file, and vise versa.

cytomapper

Visualization of highly multiplexed imaging data

cytospade

Cytoscape plugin for SPADE

cytosplore.github.io

deepcell-tf

Deep Learning Library for Single Cell Analysis

dice-xmbd

Deep learning-based cell segmentation tool for imaging mass cytometry

dimensionality_reduction-imagej

Dimensionality reduction (UMAP, t-SNE, PCA) for ImageJ/Fiji

enhancedvolcano

Publication-ready volcano plots with enhanced colouring and labeling

flowsom

Using self-organizing maps for visualization and interpretation of cytometry data

hipdynamicsr

HipDynamics is a data analytics middleware that allows you to slice multi-dimensional data sets according to a pre-defined context.

histocat

Histology Topography Cytometry Analysis Toolbox

ilastik

ilastik-shell, applets, and workflows to string them together.

imacyte

ImaCytE is an interactive tool for data-driven exploration of Imaging Mass Cytometry data as presented in the paper "ImaCytE: Visual Exploration of Cellular Micro-environments for Imaging Mass Cytometry Data".

imaxt-image

imc-nuclear-segmentation

imcdataanalysis

This repository hosts an R based workflow to perform downstream analysis of IMC data.

imcdatasets

ExperimentHub collection of imaging mass cytometry datasets

imcpluginscp

CellProfiler plugins for multiplexed image analysis

imcrtools

An R package for handling and analysing imaging mass cytometry data

imcsegmentationpipeline

A pixel classification based multiplexed image segmentation pipeline