Anne Carpenter

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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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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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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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 analysis. These tips are a bit CellProfiler-centric but generally applicable to any quantification you might do.

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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 materials such as human primary cells that are in short supply.

Might there be a shortcut allowing you to screen a huge chemical library without the expense? If you have image-based screens of a large compound set on hand, this ...

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Looking for the Unexpected: Unbiased Image Analysis

Anne Carpenter

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 The
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