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

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 realize that neither your laptop nor the old general-use computer in the lab are up to analyzing thousands (or tens of thousands, or hundreds of thousands!) of images.  But, congratulations! You’ve reached an elite level of CellProfiler users when you outgrow processing on a single local computer. Continue reading

Looking for the Unexpected: Unbiased Image Analysis

The Cell Painting assay (six stains that label eight cellular components, imaged in five channels)

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 in mind phenotypes to measure, so you use CellProfiler to accurately quantify them. But did you realize you could also measure everything you can from the images and let the data tell you what distinguishes your two conditions? Continue reading