CellProfiler: free, versatile software for automated biological image analysis.

By M. R. Lamprecht, David M. Sabatini, Anne E Carpenter. BioTechniques, 2007

953 citations recorded by the source corpus.

Careful visual examination of biological samples is quite powerful, but many visual analysis tasks done in the laboratory are repetitive, tedious, and subjective. Here we describe the use of the open-source software, CellProfiler, to automatically identify and measure a variety of biological objects in images. The applications demonstrated here include yeast colony counting and classifying, cell microarray annotation, yeast patch assays, mouse tumor quantification, wound healing assays, and tissue topology measurement. The software automatically identifies objects in digital images, counts them, and records a full spectrum of measurements for each object, including location within the image, size, shape, color intensity, degree of correlation between colors, texture (smoothness), and number of neighbors. Small numbers of images can be processed automatically on a personal computer and hundreds of thousands can be analyzed using a computing cluster. This free, easy-to-use software enables biologists to comprehensively and quantitatively address many questions that previously would have required custom programming, thereby facilitating discovery in a variety of biological fields of study.

Subfields: Biophysics, Media Technology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9fd701a40f584b8decb94bb7691ecb8d3f98d94a

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Citations in the corpus

Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software (2011, methodology): “In the four years since its publication (Carpenter et al., 2006; Lamprecht et al., 2007), it has been rapidly adopted by the worldwide biological community and cited in more than 250 articles.”
Direct Signaling Between Platelets and Cancer Cells Induces an Epithelial-Mesenchymal-Like Transition and Promotes Metastasis (2011, methodology): “(magnification 3x) and the number of cells/picture was automatically counted with Cell Profiler (Lamprecht et al., 2007).”
CellProfiler: image analysis software for identifying and quantifying cell phenotypes (2006, methodology): “We have also modified CellProfiler to measure yeast colonies, yeast growth patches, wounds in scratch assays, and tumors [ 55 ].”
Computer Methods and Programs in Biomedicine (2019, methodology): “Otsu thresholding (CellPRoﬁler [11] ) was validated because of its ability to separate foreground and background pixels.”
Histology image analysis for carcinoma detection and grading (2012, methodology): “As one example, the open source cytology image analysis software, CellProfiler [90], is designed for biologists to quantitatively measure phenotypes in thousands of images automatically.”
Advanced Level-Set-Based Cell Tracking in Time-Lapse Fluorescence Microscopy (2010, methodology): “For further comparison, we have also chosen two publicly available specialized software packages: CellProfiler [62], [ 63 ] and DCellIQ (based on [64], [65]).”
Substrate modulus directs neural stem cell behavior. (2008, methodology): “In the neuronal differentiation experiment, b-tubulin III intensity histograms were generated in CellProfiler software (38).”
ColonyArea: An ImageJ Plugin to Automatically Quantify Colony Formation in Clonogenic Assays (2014, methodology): “Alternatively, free distribution software can be employed, either as standalone solutions (CellProfiler, [12] and OpenCFU, [13]) or as macros for ImageJ (National Institutes of Health, Bethesda MD – USA) [4].”
Bioimage informatics: a new area of engineering biology (2008, methodology): “The CellProfiler system (Carpenter et al., 2006; Lamprecht et al., 2007) was developed to screen cellular images rapidly and gather information such as number of cells, size and other morphological features of cells, per-cell protein levels, cell cycle distribution, etc.”
MTBP, the partner of Treslin, contains a novel DNA-binding domain that is essential for proper initiation of DNA replication (2017, neutral): “images were loaded into CellProfiler (Lamprecht et al., 2007).”
Molecular tools in rhizosphere microbiology—from single-cell to whole-community analysis (2009, methodology): “coli recombinant clones on bacteria- or fungi-seeded agar plates subsequently analyzed to detect growth inhibition halos around the positive clones (Lamprecht et al. 2007) while other bioassays are achieved by preparing an extract from each E.”