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CellProfiler 3.0 release: faster, better, and 3D

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...

Z-score big! A game plan for image-based profiling

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...

Mo Data, Mo Problems: How to share big data with ease

Kyle Karhohs # Sharing Image Data At the Imaging Platform we frequently need to send and receive images between collaborators or forum users. Working with images can become challenging simply due to their file size. Memory and disk limitations are often irritants when analyzing images, but in some...

A Quantitative Path to Pathology

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...

Quantifying microscopy images: top 10 tips for image acquisition

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...

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

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...

Help! Why do my output images seem all black?

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...