Open-source software for exploring and analyzing large, high-dimensional image-derived data.
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Updated
Jul 21, 2025 - Python
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.
Python package for processing image-based profiling data
A pixel classification based multiplexed image segmentation pipeline
A curated list of awesome cytodata resources
Run encapsulated docker containers with CellProfiler in the Amazon Web Services infrastructure.
Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools.
Image-based Profiling Handbook
Running cellprofiler on eddie3 / SGE clusters
High-dimensional phenotyping to define the genetic basis of cellular morphology
Image-based profiling and machine learning to predict failing vs. non-failing cardiac fibroblasts
slideToolkit: a free toolset for analyzing wholeslide high-resolution digital histological images.
Single cell analysis of the JUMP Cell Painting consortium pilot data (cpg0000)
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.
ImageJ macros for preparation of single images from stacks with maximum intensity projections and partially automated selection of slices in focus. CellProfiler Pipeline for yH2AX and 53BP1 counting and mitotic cells segmentation in asynchronous cultures. R scripts for processing of CellProfiler output.
Singularity-based linux container with CellProfiler 4 pre-installed into it.
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