Why Use CellProfiler?

Most laboratories studying biological processes and human disease use light/fluorescence microscopes to image cells and other biological samples. There is strong and growing demand for software to analyze these images, as automated microscopes collect images faster than can be examined by eye and the information sought from images is increasingly quantitative and complex.

CellProfiler is a versatile, open-source software tool for quantifying data from biological images, particularly in high-throughput experiments. CellProfiler is designed for modular, flexible, high-throughput analysis of images, measuring size, shape, intensity, and texture of every cell (or other object) in every image. Using the point-and-click graphical user interface (GUI), users construct an image analysis "pipeline", a sequential series of modules that each perform an image processing function such as illumination correction, object identification (segmentation), and object measurement. Users mix and match modules and adjust their settings to measure the phenotype of interest. While originally designed for high-throughput images, it is equally appropriate for low-throughput assays as well (i.e., assays of < 100 images).

CellProfiler can extract valuable biological information from images quickly while increasing the objectivity and statistical power of assays. It helps researchers approach a variety of biological questions quantitatively, including standard assays (e.g., cell count, size, per-cell protein levels) as well as complex morphological assays (e.g., cell/organelle shape or subcellular patterns of DNA or protein staining).

The wide variety of measurements produced by CellProfiler serves as useful "raw material" for machine learning algorithms. CellProfiler's companion software, CellProfiler Analyst, has an interactive machine learning tool called Classifier which can learn to recognize a phenotype of interest based on your guidance. Once you complete the training phase, CellProfiler Analyst will score every object in your images based on CellProfiler's measurements. CellProfiler Analyst also contains tools for the interactive visualization of the data produced by CellProfiler.

In summary, CellProfiler contains:


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