CellProfiler

CellProfiler is free, open-source cell image analysis software. Its strength is in processing large numbers of images, even hundreds of thousands. In theory it can be used on images of any sort. In particular, it has been geared for scientists analyzing images of cells, a type of Microscope image processing.

Features
CellProfiler was designed to bridge the gap between sophisticated computer vision research and the average biologist, so its use does not require advanced computer skills. Users can use standard digital image processing functions on their images (e.g. crop, rotate, rescale intensity, etc.), but the real strength of the software is in its automatic identification of objects in images (usually cells). Once identified, the software measures on the order of 100 different features about the cells, including various measures of area, shape, intensity, texture, location, and count.

CellProfiler is modular, so users can put together a "pipeline" of modules to measure the cells in their images in whatever way they choose. These pipeline files are small and shareable, so colleagues can easily collaborate, and scientists can keep a pipeline as a permanent record of how their images were processed.

History
CellProfiler was released in December 2005 by scientists from the Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology. It is currently developed and maintained by the Imaging Platform of the Broad Institute.

Community
Because CellProfiler is a free, open-source project, anyone can develop their own image processing algorithms as a new module for CellProfiler and contribute it to the project. The CellProfiler Project website contains a forum for discussion where new users can have their questions answered, usually by the creators of the project.