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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...

Runxi Shen

Person: Postdoctoral Associate

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.

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...

Help! Why does CellProfiler say it can’t find any valid image sets?

Blog: January 09, 2017

Beth Cimini Defining the input to CellProfiler can be the hardest part of getting your pipeline set up and your analysis underway. Incoming images are configured in the first 4 modules of CellProfiler – Images, Metadata, NamesAndTypes, and Groups – which offer lots of flexibility. But it’s sometimes...

Making it easier to run image analysis in the cloud: announcing Distributed-CellProfiler

Blog: December 28, 2016

Beth Cimini There’s nothing more exciting than getting back a big batch of data from your automated microscope – finally, you have the results of your screen, your timelapse, or whatever you’ve spent the last weeks or months preparing. That excitement can turn to sadness quickly though when you...

Looking for the Unexpected: Unbiased Image Analysis

Blog: December 16, 2016

Anne Carpenter So you already know how to put together an image analysis pipeline to measure particular phenotypes of interest? Great! Have you ever considered looking for the unexpected? Say you are comparing two treatment conditions, such as a negative control vs. a hormone treatment. You may have...