|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.|
Brochure about CellProfiler and CellProfiler Analyst
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.
September 7, 2012 — Upcoming Joint Cell Profiler and FCS Express 4 Image Cytometry Webinar on September 25th
We are happy to announce a joint webinar presented by CellProfiler and De Novo Software teams. The back-to-back presentations will demonstrate the use of CellProfiler for running image analysis on nuclear translocation and colony counting assays and import of the results into FCS Express 4 Image Cytometry for interactive reporting for the images and data.
The webinar will be on Tuesday, September 25, 2012, 10:00 AM - 11:00 AM PDT. You may register by following this link.
- Presentation 1: Mark Bray, Ph.D., Broad Institute, "Image analysis using CellProfiler for object identification and quantification."
- Presentation 2: De Novo Software "Analysis and Reporting demonstration with Cell Profiler Data."
More details on the interface between CellProfiler and FCS Express 4 can be found here.
UPDATE (October 5, 2012): The webinar is now online at the DeNovo Software website.
Broad Bioimage Benchmark Collection (BBBC)
The Broad Bioimage Benchmark Collection (BBBC) is a collection of freely available microscopy image sets for developing and testing image analysis algorithms.