CellProfiler is free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. See our papers on analyzing cell images and non-cell images.

CellProfiler Analyst is free open-source software for exploring and analyzing large, high-dimensional image-derived data. It includes machine learning tools for identifying complex and subtle phenotypes. See our papers on data visualization and machine learning.

CellProfiler image arrow CellProfiler Analyst image

Brochure about CellProfiler and CellProfiler Analyst

CellProfiler News

January 31, 2014 — Now available: CellProfiler Annual Support and Training Plan

Gain direct access to the CellProfiler team, while supporting the CellProfiler project!

Starting in 2014, we are pleased to offer the CellProfiler Annual Support and Training Plan, a bundle of services to help you to optimize your use of CellProfiler.

Subscribing organizations will receive project-specific image assay development, training, configuration assistance, and custom software engineering to add features of interest to the open-source CellProfiler project. Support is offered by email, phone, and in-person at our laboratory in Cambridge, Massachusetts. Plus, gain access to easily installable, code-signed packages of unreleased versions of CellProfiler and 20% discounts on CellProfiler training workshops.

For more details: CellProfiler Annual Training and Support Plan

January 24, 2014 — CellProfiler 2.1.0 release!

The CellProfiler team is excited to announce the release of CellProfiler 2.1.0!

In this major update, we have made it easier to load complicated collections of images and associated data. The new version is often many times faster on computers with multiple CPU cores, so very large sets of images can now be processed on a regular personal computer. Memory handling is also improved, and there are many new image processing options, features, usability enhancements, speed improvements, and bug fixes. More details are in the release notes: https://github.com/CellProfiler/CellProfiler/wiki/CellProfiler-release-notes

January 16, 2014 — CYTO University webinar on CellProfiler now available

Mark-Anthony Bray recently presented a webinar on CellProfiler entitled "Using CellProfiler for Biological Image Analysis" for CYTO University. Check out the overview and the webinar.

May 7, 2013 — Upcoming workshop in Sweden featuring CellProfiler June 3–5

Meet our own lead software developer Lee Kamentsky and learn how to contribute to the CellProfiler project at a workshop organized by Carolina Wahlby (also one of our own) on 'How to use and make additions to open-source software for image processing, analysis, and visualization in medicine and microscopy.' June 3-5 at the Centre for Image Analysis, Uppsala University, Sweden.

Space is limited to twenty participants, so be sure to see the workshop's webpage to register soon!

May 6, 2013 — CellProfiler tutorial at CYTO 2013

Our own David Logan will be presenting a scientific tutorial on CellProfiler at CYTO 2013! Registration for the tutorial is ongoing and can be done onsite, subject to seat availability. See this forum post for more information; registration with CYTO for the tutorial can be done independently of conference registration.

March 6, 2013 — Advanced high-content analysis contribution to the Assay Guidance Manual now live!

The Assay Guidance Manual is a free, online resource provided by the National Institutes of Health to be a compilation of "best practices" in assay development for molecular screens. A section on the basics of image-based high-content screening (in which CellProfiler got a mention) has already been published, and our group was asked to put together a section on more advanced methods. The contributed chapter has just been posted online and is available here.

February 4, 2013 — Educational exercises added to the Tutorials page

We have just added a couple of educational exercises to assist new users getting started with CellProfiler and CellProfiler Analyst.

The first is a demonstration of our recently-published Worm Toolbox. The second provides details on setting up a pipeline in CellProfiler for a translocation assay and visualizing the results in CellProfiler Analyst.

Both are intended to be in-depth resources for biologists using the software for the first time, or for educators who want to introduce their students to the utility and power of image analysis. To download them, go here.

Old news…

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Funding and support for the CellProfiler project has been provided by: