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CellProfiler goes 3D

July 23, 2018

Editor's note: This article, which originally ran Oct. 16, 2017, has been updated to reflect a recent publication in PLOS Biology.

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. CellProfiler 3.0 was released in October 2017 and is the first version that can identify objects in 3D images volumetrically.

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"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 cellprofiler.org/releases/. Read Anne Carpenter's 2017 blog post on the release here.


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