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CellProfiler goes 3D

This month, researchers from Broad Institute of MIT and Harvard and the Allen Institute for Cell Science published an article in the journal PLOS Biology describing the latest iteration of a cell image processing software package, 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.


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CellProfiler 3.0 was released in October 2017 and 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,” said 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 is the result of a collaboration between Broad Institute and the Allen Institute, 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,” said Winfried Wiegraebe, Ph.D., Director of Microscopy and Image Analysis 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 at Read Anne Carpenter’s 2017 blog post on the release here.

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About Allen Institute for Cell Science

The Allen Institute for Cell Science, a division of the Allen Institute, an independent, 501(c)(3) nonprofit medical research organization, is dedicated to understanding and modeling cells: the fundamental units of life. By integrating technologies, approaches, models and data into a common standardized framework, the Allen Institute for Cell Science is creating dynamic, visual models of how genetic information is transformed into cellular behavior, and how the molecules and organelles within each cell interact and function as systems. These predictive models will enable the cell science community to better understand the role of cells in both health and disease. The Allen Institute for Cell Science was launched in 2014 with a contribution from founder and philanthropist, the late Paul G. Allen. The data, tools and models from the Allen Institute for Cell Science are publicly available online at

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