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April 13, 2008


Filed under: image processing/image analysis software, reviews — Peter @ 5:33 pm

Guest post by Ash Pahwa.

CellProfiler was developed at Whitehead Institute for Biomedical Research and MIT by Anne Carpenter’s group. This software is designed for mass processing of bio-medical images. The main focus of the software is to identify and quantify cell phenotypes. I tested CellProfiler version number 1.0.4628 published on April 23, 2007. It is an open source software that also works with Open Microscopy Environment (OME). The software is an interface tool for MATLAB and it comes with a runtime version of MATLAB.

The unique feature of CellProfiler is that it allows mass processing of images. 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, the processing starts and all the operations specified in the pipeline are performed on all the images. The result of all the operation can be exported to a database or Excel spreadsheet. However, CellProfiler does not have such database management capabilities as cellAnalyst.

The standard operations are as follows:

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

Besides these features CellProfiler also provides many other advanced image processing tools used primarily with the biomedical images. Since CellProfiler is an interface from the image processing tool box of MATLAB (IPT), all the IPT functions can also be applied to the images; for example, special filters, histogram equalization, frequency filters etc. User has the ability to write his own MATLAB scripts for custom image processing tasks. The primary market of this product is a place where images are being captured in high quantities. Individual image analysis is not possible in these conditions. In these circumstances CellProfiler can used to analyze the images while saving time as well as improving accuracy of the analysis.

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