CellProfiler is pipeline-based image analysis software specialising in object segmentation and measurement.

It incorporates many advanced algorithms for accurate segmentation and processing of objects of interest.


  • Software specialising in segmentation and analysis of objects (e.g. cells and nuclei) within images and image stacks.
  • Based on a modular design, where each process or analysis is added to the workflow pipeline.
  • Object analyses include size, shape, intensity, nearest neighbour distances and tracking.
  • Additional modules cover basic image processing, such as application of filters, generation of intensity projections and general image transformations.


  • Performs strongly in object-based processing and analysis, such as segmentation of cells stained with multiple fluorophores, colocalisation and shape measurement.
  • Modular design facilitates high-throughput for standardised imaging data.
  • Compatible with .lif image format produced by Leica LAS.


  • Limited number of additional modules available online; however, additional functionality can be added in-house.
  • Currently has partial support for 3D segmentation; however, this is being improved with the latest releases.


  • Guidelines for citing CellProfiler can be found here.


  • Open source and free to download.
  • Requires installation by IT Services.
  • Free half-day workshops are held regularly to help researchers learn to construct analyses with CellProfiler.

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