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

A pixel classification based multiplexed image segmentation pipeline

Python package for processing image-based profiling data

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

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

A curated list of awesome cytodata resources

Image-based Profiling Handbook

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

Tools for Processing Results from CellPainting Assay

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

Image-based analysis of cardiac fibroblast datasets to uncover proprietary drug impact on reversing fibrosis

analyzing CellProfiler output

Running cellprofiler on eddie3 / SGE clusters

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

“Novel Marker Distribution Pipeline for Analysis of Cell Based Quantitative Spatial Information”. The aim of this research was to analyse quantitative spatial information and provide intuitive visualisation relating to the identification of cells relative to tissue structure and pathology such as cancer tumour.

Collect distributed cellprofiler results into sqlite databases.

Documentation and scripts to install CellProfiler on eddie3

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

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