Shantanu Singh
I lead the image-based profiling team. We develop machine learning and statistical methods to create fingerprints of genes, chemicals, and diseases from microscopy images of cells.
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Press from the Imaging Platform (Carpenter-Singh and Cimini labs)
Impact of CellProfiler on human health Our CellProfiler software has yielded discoveries in several translational projects, some of which may ultimately have a direct impact on the treatment of disease [ read more here]. Public videos of talks and PDF slides Links to PDFs of slides from recent talks...
Papers
For our latest work, check out our preprints on bioRxiv! ( Carpenter) ( Singh) Google Scholar pages (with citation metrics): ( Carpenter) ( Singh) 212. Rouquié D, Bender A, Cheah J, Crute C, Dalmas D, Ewald J, Fullerton A, Harrill JA, Kadri S, Kleinstreuer N, Kramer N, LaRocca J, Mitchell CA, Seal S...
Meet Our Team
CellProfiler 4.0 Release: Improvements in speed, utility, and usability
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...
Contact
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
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
Group Alumni
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...
Research
We are passionate about developing computational techniques that accelerate the discovery of new medicines, and we work across all disease areas, from cancer and psychiatric disease to rare disorders and infectious disease. A major focus is image-based profiling: we invented CellProfiler and the...