In Summary CellProfiler provides a ‘test mode’ so you can compare several algorithms and choose the best module and settings to get the best result. They document the amount of digital image processing noise and the importance of gathering computational provenance information. Then use the ExportToSpreadsheet module, to export the intensity measurements for each object to an excel file. The output of this procedure was 136 SQLite files (one for each plate) representing unnormalized single-cell profiles. All these numerical results are available at and are traceable to image objects. Briefly, we applied a CellProfiler image analysis pipeline to segment cells, adjusted for background intensity, and measured morphology features for three compartments: cells, cytoplasm, and nuclei. Shape and textural feature variations had a negative impact on classification outcomes in 52.9% and 97.1% of all single feature-based classifications, respectively. This unit outlines the use of CellProfiler, a free, open-source image analysis tool that extracts quantitative information from biological images. Questions (27) Publications (2,645) Questions related to Cell Profiler. By characterizing feature variations across Python scikit-image, CellProfiler, MaZda, ImageJ, and in-house Java libraries, we concluded 15.6% of 32 intensity features, 47.9% of 71 shape features, and 88.2% of 68 textural features differ in values. Visual analysis is required to perform many biological experiments, from counting colonies to measuring the size or fluorescence intensity of individual cells or organisms. Explore the latest questions and answers in Cell Profiler, and find Cell Profiler experts. The objective is to highlight the sources of digital image processing variability when deriving image-based scientific conclusions. Our motivation is to introduce readers to image-based object measurements and to quantify numerical variability of image features and feature-based classification outcomes.
This chapter addresses object measurements from 2D microscopy images.
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