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CellProfiler goes 3D

October 16, 2017

The Broad Institute of MIT and Harvard and the Allen Institute for Cell Science today announced the release of CellProfiler 3.0. CellProfiler is a free, open-source quantitative image analysis package developed by Broad Institute scientist and Imaging Platform director Anne Carpenter, Ph.D., and her team. CellProfiler 3.0 is the first version that can identify objects in 3D images volumetrically.

“The field of cell biology has been waiting for an open access image analysis software capable of handling high-replicate three-dimensional data sets,” says Susanne Rafelski, Ph.D., Director of Assay Development at the Allen Institute for Cell Science. “Cells are by nature three-dimensional. This new generation of CellProfiler will allow researchers to capture their behavior more fully.”

Eighteen months in the making, CellProfiler 3.0 the result of a collaboration between Broad Institute and the Allen Institute for Cell Science, which funded the project together with the National Institutes of Health. Many researchers require completely automated analysis of 3D images. The new capabilities of CellProfiler aim to address this growing need.

“We’re trying to understand and model the organization and behavior of human stem cells,” says Winfried Wiegraebe, Ph.D., Director of Microscopy at the Allen Institute for Cell Science. “This requires us to capture and process large 3D image datasets. Working with the Broad Institute to develop CellProfiler 3.0, we now have a tool that can do that 3D image processing much more efficiently.”

CellProfiler 3.0 is available for download now at Read Anne Carpenter’s blog on the new release here.