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Anne Carpenter We are thrilled to announce that CellProfiler 3.0 is now released! Download it here. Eighteen months in the making, this is the first version of CellProfiler that can identify objects in 3D images volumetrically – the result of a collaboration with the Allen Institute for Cell Science...

Anne Carpenter Not every image you capture on your microscope is suited for quantification, no matter how nice they may look. Even though you might not notice any problems by eye, the tips outlined here for acquiring and storing images can improve the quality of data derived from digital image...

Beth Cimini Double clicking on the output images produced by CellProfiler sometimes opens up a screen in your operating system’s default image viewer that looks all black. This can make it seem like your pipeline didn’t work or didn’t produce the right output. However, this can happen for a couple...

Minh Doan Thanks to the rapid advancement in image processing, we now have so many techniques to characterize cellular and subcellular objects (hooray CellProfiler!) Measuring cultured cells in monolayers is (usually) easy…but what about examining how cells interact with each other and their...

Beth Cimini Everyone here at the CellProfiler team is very excited about our new 3.0 release, and we certainly hope you are too! CellProfiler 3.0 is much faster than any of our previous releases, and the addition of volumetric processing is a huge game changer. CellProfiler 3.0 looks pretty similar...

Juan Caicedo As described in our lab’s recent review article, there are so many great reasons to use microscopy images to create signatures of perturbations: identifying phenotypes associated with disease, identifying chemical mechanisms of action, and discovering gene functions, among others. Have...

Guest Author This post was written by a guest author, Kun-Hsing Yu, who can be reached at Kun-Hsing_Yu@hms.harvard.edu. Lung cancer causes more than 1.4 million deaths per year. To diagnose lung cancer, pathologists prepare microscopic slides from surgical or biopsy samples, stain them with...

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...

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...

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...