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.
• Currently has partial support for 3D segmentation; however, this is being improved with the latest releases.

Citing

• Guidelines for citing CellProfiler can be found here.

Availability

• 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.

Additional information

• CellProfiler course material
• Download CellProfiler
• Wikipedia