CellProfiler

CellProfiler is software intended for developing a workflow of complex image analysis tasks in cell biology and related fields.

was developed at Whitehead Institute for Biomedical Research and MIT by Anne Carpenter’s group. This software is designed for mass processing of biomedical images. The main focus of the software is to identify and quantify cell phenotypes. The software is an interface tool for MATLAB and it comes with a runtime version of MATLAB.

The most important feature of CellProfiler is that it allows mass processing of images. The user specifies two items. First, the folder name where the images are stored. And second, a list of operations that need to be performed on the images. This list of operations is called a “pipeline”. Once both items are specified, all the operations specified in the pipeline are performed on all the images in the folder. The result of all the operation can be exported to a database or Excel spreadsheet.

The standard operations are:

Cell counting,
Cell size,
Cell identification,
Per-cell protein levels,
Cell shape,
Sub-cellular levels of DNA,
Protein staining.

In addition to these features, CellProfiler also provides many other image processing tools used primarily with the biomedical images. Since CellProfiler is an interface with MATLAB, all functions of the Image Processing Toolbox are also available: filters, histogram equalization, frequency filters etc. The user can write his own MATLAB scripts for custom tasks.

The primary use for CellProfiler is in a place where images are captured in high quantities and manual analysis is impossible.

Example is below with the the images copied from CellProfiler's site followed by pictures produced by Pixcavator (see Particle and cell analysis).