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Leveraging advanced segmentation models in CellProfiler with RunCellpose and RunStarDist

Blog: June 12, 2024

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...

Tim Treis

Person: Visiting Scholar

I'm a 2nd year PhD student at the Theislab in Munich, Germany. There, my primary focus is development of tools and resources for spatial multi-omics. At the Broad to learn more about xxx terabyte scale data and how we can use phenomics to better understand perturbations.

Hugo Hakem

Person: MLSC Intern

After graduating from UC Berkeley and Ecole Centrale Paris, I am currently an MLSC intern focusing on gaining biological insights from cell profiles using counterfactuals and deep learning tools. I am enthusiastic about utilizing my background in mathematics and computing to contribute to the drug...

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...

Browser-based Apps for Data Visualization

Blog: February 07, 2019

Minh Doan Have you ever stumbled across some amazing data visualization tools that run entirely on a web browser (such as this and many others), and wished you could plug in your own data and visualize it? Or, as a biologist, you may know of a good analytic tool, but it either costs too much...

The CellProfiler 2 User’s Guide to CellProfiler 3.0, Part II: Converting your pipelines

Blog: October 24, 2017

Beth Cimini For those of you who’ve been with us for a long time though, the obvious next question after how to use the new test mode is will my old CellProfiler pipelines work in the new version? We feel the same way – the pipelines you’ve accumulated over the years are precious resources! The good...

It is plane to Z how FIJI is a great companion for visually verifying CellProfiler’s 3D segmentation

Blog: April 11, 2017

Kyle Karhohs Now that CellProfiler can handle 3D images, how do you view the results? When processing 2D images, the IdentifyPrimaryObjects module will produce a figure that displays the original image next to the segmented image to make validation fast and convenient, a side-by-side comparison...

Screening a million compounds for the price of a few thousand?

Blog: April 05, 2017

Anne Carpenter Biologists are coming up with more and more complex physiologically-relevant assay systems and scaling them up for screens. From co-cultured cells to C. elegans to 3D organoids and tumor spheroids, these assay systems can be challenging, expensive, lower-throughput, and/or rely on...

CellProfiler & Ilastik: Superpowered Segmentation

Blog: January 19, 2017

Kyle Karhohs Joining forces CellProfiler is capable of accurate and reliable segmentation of cells by utilizing a broad collection of classical image processing methods. Peruse the documentation on the IdentifyPrimaryObjects module, for example, to get a sense of these, e.g., thresholding...