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

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 and bad news is that the answer is Yes, mostly. In order to facilitate the speedup and continue the process of streamlining the code, a few things had to go; we also removed some things we felt were causing “option fatigue” for the sake of user friendliness going forward.

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Help! Why do my output images seem all black?

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 of reasons:

(a) If you’re exporting objects and have only a few objects in your image
(b) If you’re exporting 16-bit images

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

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 confusing what each one does, and it’s not always obvious which ones you need for your experiment. Continue reading

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