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

A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.

A pixel classification based multiplexed image segmentation pipeline

Python package for processing image-based profiling data

A curated list of awesome cytodata resources

Run encapsulated docker containers with CellProfiler in the Amazon Web Services infrastructure.

Image-based Profiling Handbook

Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools.

High-dimensional phenotyping to define the genetic basis of cellular morphology

slideToolkit: a free toolset for analyzing wholeslide high-resolution digital histological images.

Running cellprofiler on eddie3 / SGE clusters

Single cell analysis of the JUMP Cell Painting consortium pilot data (cpg0000)

Image-based profiling and machine learning to predict failing vs. non-failing cardiac fibroblasts

analyzing CellProfiler output

Tutorial for single cell analysis of nuclear translocation measured by timelapse imaging

Tools for Processing Results from CellPainting Assay

Install script for CellProfiler v3.1.9 on Ubuntu 18.04.3 LTS(+) - bash, installs python3.6, unet and classify

CellProfiler pipeline and ImageJ workflow developed for segmentation of H2B_FUCCI2a_MCF7 cell nuclei for per-nucleus and background fluorescence intensity measurement. Example workflows for downstream cell cycle analysis are also provided in this repository.

Singularity-based linux container with CellProfiler 4 pre-installed into it.