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.