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Getting Started with CellProfiler in Batch

Blog: May 18, 2020
Guest Author This post was written by a guest author, Jillian Rowe, who can be reached at jillian@dabbleofdevops.com. Running CellProfiler in batch mode is the ideal way to automate large scale analyses. Or not so large scale analyses that you prefer to automate! One of the benefits of running...

Positions available

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Sabbaticals We welcome professors to our group as visiting scientists for sabbaticals. Please contact imagingadmin(at)broadinstitute.org for more information. Other Positions We welcome inquiries from top-notch scientists with experience at all levels. Please send CV and statement of interest to...

CellProfiler 4.0 Release: Improvements in speed, utility, and usability

Blog: September 09, 2020
David R. Stirling We have now released CellProfiler version 4.0! Download it here. The primary goal of this release has been to migrate CellProfiler from Python 2 to Python 3. This has involved extensive restructuring of the code base, leading to a lot of “under-the-hood” improvements. Important...

Research

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Our main research theme is quantifying and mining the rich information present in cellular images to yield biological discoveries, often using deep learning. We work on high-throughput projects (100,000-1,000,000 images) probing a variety of biological processes and diseases of interest, with a...

Contact

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Email imagingadmin@broadinstitute.org Mailing address Broad Institute of MIT and Harvard415 Main StreetCambridge, MA 02142Our offices are on the 5th floor of 415 Main St [ Google Maps link]. Look for the entrance of our building to the right of the Broad Institute sign.

NSF CAREER project page

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NSF CAREER Award Project (March 2012–February 2017) [ Project abstract at nsf.gov] [Project Outcomes Report (search here, using Fed Award ID 1148823 ( PDF))] Non-technical description of the problem: Biologists want to test genetic and chemical treatments in environments that more closely mimic the...

Anne E. Carpenter

Person: Principal Investigator, Institute Scientist, Senior Director of the Imaging Platform

Group Alumni

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Where are they now? Check their career progress on Dr. Carpenter's [ CV] Note: the Carpenter lab became the Carpenter-Singh lab in 2021. Alum Years Role Adam Fraser 2008–2011 Lead software developer for the CellProfiler Analyst project Adam Papallo 2005–2007 Bioinformatics Analyst Adeniyi Adeboye...