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CellProfiler

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 by Anne Carpenter

Suggested by: Roy Winters

Description

CellProfiler is an open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

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Anne Carpenter
Principal Investigator (PI) at Broad Institute of Harvard and MIT
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Anne Carpenter

Principal Investigator (PI) at Broad Institute of Harvard and MIT

When should you try CellProfiler? Oval 17

CellProfiler was designed for high-throughput imaging projects, so it can handle millions of images. But, we find thousands of biologists use it for small-scale biology research. If you want to extract information from images in an automated, reliable, quantitative way, download an example pipeline from CellProfiler's site (http://cellprofiler.org/examples.html) and adapt it to your needs. If you get stuck, check out CellProfiler's online Q&A forum.

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Posted: 4 years ago
Roy Granit
Co-founder at LabWorm
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Roy Granit

Co-founder at LabWorm

Thanks @Anne.Carpenter.76 for this introduction, and for building CellProfiler! I personally love it, and used it quite a lot in my research to quantify cell populations in tumors sections.

Are you willing to share with us what are you guys currently working on so we can know what to expect to see on CP in the upcoming future?

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Posted: 4 years ago
Anne Carpenter
Principal Investigator (PI) at Broad Institute of Harvard and MIT
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Anne Carpenter

Principal Investigator (PI) at Broad Institute of Harvard and MIT

Glad you're finding it useful @rgranit !

Sure thing. You can always check what is coming next here on our Roadmap: https://github.com/CellProfiler/CellProfiler/wiki/CellProfiler-roadmap

As of this writing, our main focus is to add 3D segmentation and measurement to CellProfiler (finally!) thanks to a collaboration with the Allen Institute for Cell Science. We also are doing a ton of much-needed maintenance on the innards of CellProfiler - this won't yield many visible changes but is critical for the ongoing health of the software.

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Posted: 4 years ago
Roy Granit
Co-founder at LabWorm
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Roy Granit

Co-founder at LabWorm

Happy to hear about the release of CellProfiler V3 with the promised 3D features broadinstitute.org/blog/cellprofiler-goes-3d Hope to check it out soon, keep it up %uD83D%uDC4D

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Posted: 2 years ago
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Associated keywords

Microscopy Computers Programming Phenotype Software Imaging

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