CellProfiler

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.

Features

  • 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.

Advantages

  • 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.

Disadvantages

  • Limited number of additional modules available online; however, additional functionality can be added in-house.
  • No native capacity for segmentation of objects in 3D (i.e. XYZ image stacks).

Availability

  • Open source and free to download.
  • Requires installation by IT Services.

Additional information

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