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

analyzing CellProfiler output

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

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

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

Tools for Processing Results from CellPainting Assay

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.