Open-source software for quantitative analysis of biological images.

  • Automated analysis
  • Can measure multiple properties at once
  • No prior experience in programming required
  • Can be run in batch mode to automate large scale analyses (see details here).
  • Compatible with Windows, Mac and Linux
  • Interfaces with ImageJ, Ilastik, OMERO, KNIME, and others
  • Opens 180+ file formats


Using CellProfiler

Human cells
Drosophila cells
Comet assay
Counting and scoring
Yeast colony classification
Yeast patch identification
Tissue neighbours
Wound healing
Illumination correction
Colocalisation analysis
Human cytoplasm-nucleus translocation
Imaging flow cytometry
Speckle counting
Object tracking
Worm toolbox