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...
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...
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...
Building a container image with Podman
Authors: Esteban Miglietta and Nodar Gogoberidze In a previous post, we have already discussed what Docker containers are and how to build them. Here, we're going to talk about an alternative to Docker for managing containers: Podman. But first... What are software containers? Software containers...
Announcing CellProfiler 3.1.9
Beth Cimini Hello all! It’s been a crazy last few months for the CellProfiler team, as we’ve been hiring some new members to the team and working hard on the transition to Python 3, which will bump us into CellProfiler version 4. Keep your eyes peeled for exciting content in the future! We did want...
Tricks for maintaining your CV/resume with Google Docs: easy to edit, immediately published
Jeanelle Ackerman You’ve earned degrees, authored papers, mentored supervisees, and traveled far and wide to speak about your work… And ideally it’s nicely showcased in your resume or curriculum vitae (CV), all updated and ready to go. But, if you’re like most academics, your CV is a sorely outdated...
Annotating Images with CellProfiler and GIMP
Kyle Karhohs Annotated image data is valuable for assessing the performance of an image processing pipeline and as training data for machine learning methods such as deep learning. When assessing the performance of a CellProfiler pipeline, for example a pipeline that segments nuclei, the annotated...