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Our CellProfiler software has yielded discoveries in several translational projects, some of which have had 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...

The CellProfiler project team is based in the Cimini Lab at the Broad Institute of MIT and Harvard. The project was started in 2003 by Anne E. Carpenter and Thouis (Ray) Jones in the Sabatini Laboratory (Whitehead Institute for Biomedical Research) and Golland laboratory (MIT’s CSAIL) and is...

CellProfiler Analyst (CPA) provides tools for classifying biological images and exploring and visualizing multidimensional data (particularly from high-throughput experiments) that has been extracted from companion image analysis software CellProfiler. CellProfiler Analyst’s primary tools: Image...

The app requires JDK 1.8 to be installed Stable (2.2.0): January 21, 2016 OS X Windows 32-bit 32-bit Source Nightly (2.2.1): OS X Windows 32-bit 32-bit Source Legacy (2.0.0): OS X Windows 32-bit 32-bit

How to cite CellProfiler in publications (the project's survival depends on it!) CellProfiler for cells (feel free to cite the most recent) : Stirling DR, Swain-Bowden MJ, Lucas AM, Carpenter AE, Cimini BA, Goodman A (2021). CellProfiler 4: improvements in speed, utility and usability. BMC...

Imaging flow cytometry (IFC) combines the high-throughput capabilities of conventional flow cytometry with single-cell imaging. CellProfiler can be used to analyze the resulting images from imaging flow cytometry, whether brightfield, darkfield, or fluorescence. We here provide an open-source IFC...

A component of CellProfiler cell image analysis software The WormToolbox is a toolbox for high-throughput screening of image-based Caenorhabditis elegans phenotypes. The image analysis algorithms measure morphological phenotypes in individual worms and are effective for a variety of assays and...

OLD CellProfiler example images and pipelines (Prior to 4.0) These examples are outdated, please see our current Examples page for the updated versions. Basic Pipelines Human cells Fruit fly cells Tumors Comet assay Specialized Pipelines Cell/particle counting and scoring the percentage of stained...