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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...

NSF BBSRC Imaging Flow Cytometry Project

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NSF BBSRC Imaging Flow Cytometry Project (July 15, 2015–June 30, 2018) [ Project abstract at nsf.gov] [Project Outcomes Report (search here, using Fed Award ID 1458626 ( PDF))] Non-technical description of the problem: There are a variety of cell types circulating in human blood, each with distinct...

Promo Images

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Biographical images are available here with credits noted in each folder name. Permission to use those or any images on this page must be requested via imagingadmin@broadinstitute.org.

Software and code

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DeepProfiler DeepProfiler is a set of tools that allow you to use deep learning for analyzing imaging data in high-throughput biological experiments. Documentation and instructions for DeepProfiler can be found in our Handbook and the code is located on the GitHub page. Cytominer The Pycytominer...

Shantanu Singh

Person: Principal Investigator, Senior Group Leader
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.

Press from the Imaging Platform (Carpenter-Singh and Cimini labs)

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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

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For our latest work, check out our preprints on bioRxiv! ( Carpenter) ( Singh) Google Scholar pages (with citation metrics): ( Carpenter) ( Singh) 194. IGVF Consortium.(2024) Deciphering the impact of genomic variation on function. Nature 633, 47–57. https://doi.org/10.1038/s41586-024-07510-0 PMID...