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CellProfiler and CellProfiler Analyst Our lab previously launched and led the CellProfiler and CellProfiler Analyst projects, beloved by biologists around the world for bioimage analysis and cited over 15,000 times. They are now developed and maintained by the Cimini lab (since 2021). DeepProfiler ​...

CellProfiler is free, open-source software for quantitative analysis of biological images. No prior experience in programming or computer vision is required – this page is intended to help you get up and running. The quickest way to get up and running with CellProfiler is to: Download CellProfiler...

Previous Examples Previous examples (prior to 4.0) can be found on the previous examples page, but we discourage their use because they are now outdated.

To reasonably compare, or benchmark, algorithms for image analysis, researchers must agree on a common reference point—the image set's "correct" answer—and see how closely each algorithm matches it. We adopt the common term ground truth for this reference point even though it may be questionable in...

Accession number BBBC002 · Version 1 Example image Biological application Five different samples of Drosophila melanogaster Kc167 cells were stained with Hoechst 33342, a DNA stain. The last sample (labeled nodsRNA) is of wild-type cells. Each of the other four samples (labeled 48, 340, Anillin, and...

Accession number BBBC006 · Version 1 Example images Ground truth: in focus Out of focus Ground truth: foreground Biological application Since robust foreground/background separation and segmentation of cellular objects (i.e., identification of which pixels below to which objects) strongly depends on...

Accession number BBBC019 · Version 2 Example images DIC image Ground truth DIC image Ground truth Biological application The wound-healing assay is considered the gold standard for studying cell motility and migration. The assay is performed by time-lapse imaging (usually by phase contrast, or...

Accession number BBBC024 · Version 1 Example images 3D image 3D foreground Biological application One of the principal challenges in counting or segmenting nuclei is dealing with clustered nuclei. To help assess algorithms' performance in this regard, this synthetic image set consists of four...

Accession number BBBC025 · Version 1 Morphological profiles of RNAi-induced gene knockdown are highly reproducible but dominated by seed effects Abstract: RNA interference and morphological profiling - the measurement of thousands of phenotypes from individual cells by microscopy and analysis image...