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Lee Kamentsky: High-throughput image analysis with CellProfiler and ImageJ


CellProfiler ( is open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. The Carpenter Lab has recently released CellProfiler 2.0, a redesign of the original software with improved reliability and functionality. One of the goals of CellProfiler 2.0 is to create interfaces to other imaging software.

The ImageJDev group is modifying the architecture of ImageJ to support efforts such as ours. The improvements will include models of image segmentation and measurement, support for scripting, headless operation of ImageJ and mechanisms for finding named images and regions of interest within ImageJ. Once these improvements are in place, CellProfiler will be able to share its segmentation, measurements and images with ImageJ in a straightforward manner.

Our first interface between CellProfiler and ImageJ allows biologists to use ImageJ macros and plugins within the high throughput-oriented environment of CellProfiler. Users can now seamlessly run ImageJ macros and plugins as part of a CellProfiler image processing pipeline and can exchange images between the two applications. We will add segmentation and measurement exchange as the project progresses.


ImageJ, CellProfiler, High-content Screening

Administrative data

Presenting author: Lee Kamentsky
Organisation: Broad Institute, UW-Madison LOCI, MBL at Woods Hole

co-authors: Curtis Rueden, Grant Harris, Adam Fraser, Anne Carpenter, Kevin Eliceiri

Biography: Lee Kamentsky is the lead software developer for CellProfiler and a participant in ImageJDev.

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