![]() The researcher creates an analysis pipeline from modules that find cells and cell compartments, measure features of those cells to form a rich, quantitative dataset that characterizes the imaged site in all of its heterogeneity. The percentage of positive nuclei vs total number of nuclei can then be computed using the CalculateMath Module.ĬellProfiler is free, open-source software for quantitative analysis of biological images.ĬellProfiler is designed to enable biologists without training in computer vision or programming to quantitatively measure cell or whole-organism phenotypes from thousands of images automatically. If needed, nuclei can be expanded in order to include touching object rather than object inside only. ![]() Nuclei are then filtered according to the property of having histone (positive) or not having histone (negtiveobject) related to them. Then objects (nuclei) are related to the second object (Histone), to create a parent child-relation ship: where nuclei can have histone has child. In a few words, it used the IdentifyPrimaryObject module of CellProfiler to detect nuclei from a channel (e.g DAPI), then again the same module on another channel to detect another probe (e.g some particular histone). This pipeline shows how to do both of these tasks, and demonstrates how various modules may be used to accomplish the same result. CP is commonly used to count cells or other objects as well as percent-positives, by measuring the per-cell staining intensity. This one example workflow from the Cell Profiler(CP) Examples.
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