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.

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Brochure about CellProfiler and CellProfiler Analyst

CellProfiler News

July 25, 2014 — CellProfiler 2.1.1 release

The CellProfiler team is pleased to announce the release of CellProfiler 2.1.1. This is a scheduled patch release whose primary purpose is to address any issues in 2.1.0.[more details]

July 2, 2014 — CellProfiler NIH grant has been renewed!

Great news! We are pleased to announce that the NIH will continue to support CellProfiler through 2018 (R01 GM089652). We are grateful that NIH recognizes the community value of open source tools and the variety of research that widely benefits from their continued maintenance. [more details]

April 30, 2014 — Impact of CellProfiler on human health

Our CellProfiler software has yielded discoveries in several translational projects, some of which may ultimately have a direct impact on the treatment of disease. For example, CellProfiler has been used to identify several small molecules that are effective in treating particular diseases in mouse models. In some cases, discoveries made using CellProfiler have even led to planning clinical trials in humans, which could directly improve patient outcomes. [more details]

April 30, 2014 — WormToolbox tutorial videos now available

Tutorial videos for the WormToolbox detailed in a recent publication in Methods are now accessible here at CellProfiler.org/WormToolbox.

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.

Old news…

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