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| 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 11, 2011 — Image Analysis Course Announcements
Our own Carolina Wählby will be teaching a course in biomedical image analysis during August/September in in Brno, Czech Republic. See here for more details on how to sign up.
Carolina will also be teaching a pre-conference course on "Microscopy Imaging Analysis - quantitative analysis of large-scale biological image data" for the Bio-IT World Europe Conference to be held in Hannover, Germany in October.
June 28, 2011 — CellProfiler Analyst 2.0 r11306 Released
This release is meant to replace r11246 which had a couple of issues detailed here.
June 21, 2011 — Upcoming Joint Cell Profiler and FCS Express 4 Image Cytometry Webinar on July 26
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, July 26, 2011, 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 (August 1, 2011): The webinar is now online at the DeNovo Software website.
June 6, 2011 — CellProfiler Analyst 2.0 r11246 Released
Introducing CellProfiler Analyst r11246. This release addresses some bugs and includes several new features including gating in the plotting tools, annotation tools in PlateViewer, a normalization tool, and improved handling of multiple database tables. Read more here or download it now here.
March 3, 2011 — CellProfiler 2.0 r10997 Released
We have released CellProfiler 2.0 r10997. The Windows release also includes an integration with the Ilastik pixel classifier. Read the complete release notes for details or download the new version.
February 2, 2011
CellProfiler is increasingly compatible with a number of open-source and commercial software projects, including National Institutes of Health's ImageJ and De Novo Software's FCS Express 4. See our new Interfaces page for details.
October 20, 2010 — Cellprofiler 2.0 r10415 Released
A new version of CellProfiler has been released. The new version provides better image handling (stability, transparancy, multi-channel TIFFs, grouping of movie frames, and loading by order). A new module for unmixing colors can be useful for histologically stained images. Granularity measurements can now be made for each object. It is now possible to call ImageJ on both Windows and Mac. There is a new metadata editor. Finally, a new splines background calculation has been added to CorrectIllumination_Calculate. Read the complete release notes for details, or download the new version.
October 1, 2010 — CellProfiler Analyst 2.0 r10530 Released
A new version of CellProfiler Analyst has been released which addresses several bugs and introduces many new features including the ability to save and load workspaces, edit Classifier's training rules, save and load tables to/from your Database and CSV files seamlessly, create per-image filters on the fly, and create box plots. Read more here or download it now here.
March 29, 2010 — CellProfiler 2.0 Released
Our image analysis software CellProfiler has been completely redesigned and written in Python, and is available for download. New features include a sparkling new graphical interface, a test mode for experimenting with module settings, improved algorithms and more.
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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.
Funding and support for the CellProfiler project has been provided by:
