Blog

Announcing CellProfiler 3.1.8

Beth Cimini

Happy holidays to everyone- we here at the CellProfiler team got you a little end-of-year treat in the form of CellProfiler 3.1.8.  This is primarily a bugfix release, getting rid of some bugs in MeasureObjectIntensity, MeasureColocalization, ExportToSpreadsheet, CorrectIlluminationCalculate, and Smooth.  We’ve also updated how we package for Windows, so those of you who had JAVA_HOME issues with 3.1.5 (feel free to now unset that in your environment variables if it’s set to your 3.1.5 install!) should now experience...

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ScienceSnippets: Building communication skills and sharing what you love

Anne Carpenter

Clearly communicating the impact of your research is one of the most important skills you need to develop as a scientist, and yet typically it is only taught by doing (and if you are lucky, feedback – especially critical feedback). Clear communication is important to get funding and resources for your work, to publish it, to entice collaborators, to impress colleagues and supervisors, … and to not be boring at parties when asked “So what do you do?”

With the help of the Broad Communications lab, I put together an...

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Tricks for maintaining your CV/resume with Google Docs: easy to edit, immediately published

Jeanelle Ackerman

You’ve earned degrees, authored papers, mentored supervisees, and traveled far and wide to speak about your work… And ideally it’s nicely showcased in your resume or curriculum vitae (CV), all updated and ready to go. But, if you’re like most academics, your CV is a sorely outdated PDF and upon its request, you always find yourself scrambling to dig up recent accomplishments to prove you’ve not just been lounging around for the last 6 months (or years). And updating it requires locating an elusive latest version of a Word...

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Announcing CellProfiler 3.1

Beth Cimini

I’m excited to announce the release of CellProfiler 3.1.

Our focus for CellProfiler 3.1 was polishing features and squashing bugs introduced in CellProfiler 3.0. We also started laying down the foundation for our next release, CellProfiler 4.0, that will transition CellProfiler from Python 2 to Python 3, improve multiprocessing, and overhaul the interface.

There’re a few noteworthy changes that some users might enjoy like UTF-8 pipeline encoding, a simpler application bundle (that won’t require installing...

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Tracking projects with Gmail tags: Collaborating through email

Anne Carpenter

As the PI of the Carpenter lab (a.k.a. Broad Institute Imaging Platform, including the CellProfiler team), people often ask how I manage so many ongoing collaborations: we discuss 50+ external projects each year so it is a lot to track! I am happy to reveal our secrets.

The goal


First, let me describe the problem we are trying to solve: we need a way/place to post project updates, raw data, and emails about a given project, so everyone in the lab can have access to info (most...

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The CellProfiler 2 User’s Guide to CellProfiler 3.0, Part I: Using the new Test Mode

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 to what you’re used to, albeit a bit sleeker than previous versions. While most of it still behaves exactly how you’re used...

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

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 and bad news is that the answer is Yes, mostly. In order to facilitate the...

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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 Science who funded the project together with NIH. If you’ve not yet seen it, the Allen Cell Explorer is a real visual and biological...

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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 you wanted to give this approach a try, but been overwhelmed by the computational options available?

Our recent paper, ...

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