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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How to Normalize Cell Painting Data
Rebecca Senft Workflow update June 2024 update Our recommended normalization workflow is evolving. Please see https://github.com/broadinstitute/jump-profiling-recipe/ for our latest developments on the normalization strategy in specific and aprofiling workflow in general. How to Normalize Cell...
Leveraging advanced segmentation models in CellProfiler with RunCellpose and RunStarDist
Segmentation is an integral step of any bioimage analysis workflow, which involves delineating areas or objects of interest within an image 1 . All the measurements performed on the image, e.g. size, shape, counts, or pixel intensities are then assigned to these segmented areas or objects to...
Papers
For our latest work, check out our preprints on bioRxiv! ( Carpenter) ( Singh) Google Scholar pages (with citation metrics): ( Carpenter) ( Singh) 198. Seal S, Trapotsi MA, Spjuth O, Singh S, Carreras-Puigvert J, Greene N, Bender A, Carpenter AE. (2024) Cell Painting: a decade of discovery and...
Runxi Shen
I focus on developing advanced deep-learning methods to create robust cell representations from cell painting assays. My research aims to understand how various genetic variants alter cellular states and explore potential treatments for diseases associated with these variants.
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...