CellCognition protocols

View CellCognition computational protocol

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CellCognition specifications

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Unique identifier OMICS_06486
Name CellCognition
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for CellCognition

CellCognition in pipeline

2017
PMCID: 5223612
PMID: 27940887
DOI: 10.1083/jcb.201610026

[…] sets of feature extractors with modular segmentation pipelines into software platforms that are publicly available and widely used (). specific examples of popular platforms include cellprofiler (), cellcognition (), and phenoripper (). outputs from these platforms typically contain hundreds to thousands of different features for each object and image. although these methods are mostly […]


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CellCognition in publications

 (18)
PMCID: 5923496
PMID: 29670029
DOI: 10.3390/v10040202

[…] in a biomedical imaging context, ml is typically used for relatively simple tasks, such as segmentation, tracking, denoising, and phenotype determination. for example, tools like ilastik [] and cellcognition provide easy-to-use and powerful ways to segment and classify of images by reinforced machine learning []., recent advances in computing, specifically in graphical processing units, […]

PMCID: 5577222
PMID: 28855639
DOI: 10.1038/s41598-017-10088-5

[…] through mitosis. drg1 expression was down-regulated by sirna. 24 hours post-transfection, live-cell imaging was carried out for 48 hours (fig. ). analysis of chromatin features using the software cellcognition showed that the time from prophase to anaphase onset was extended upon drg1 downregulation as compared to the control conditions (fig. ). analyzing the spindle features showed […]

PMCID: 5109238
PMID: 27707753
DOI: 10.15252/embj.201694056

[…] the normal vector of the best‐fitting plane for the ventricular surface was calculated using r scripts as described before (postiglione et al, )., automated image analysis was performed using the cellcognition software (held et al, ) (http://www.cellcognition.org), based on a previously established processing pipeline to determine mitotic duration (schmitz et al, ). cell nuclei and mitotic […]

PMCID: 5021097
PMID: 27597760
DOI: 10.1083/jcb.201605024

[…] t′ = t − t0., the numbers of mrna per cell were counted manually for and . to quantify single mrna molecules and mrna blobs in , we used an automated pipeline. cell segmentation was performed with cellcognition (), using dapi for nuclear segmentation and the smfish images for cellular segmentation with a watershed method. fluorescent spots were detected with fish-quant (), with the connected […]

PMCID: 4947524
PMID: 27362226
DOI: 10.1038/nature18610

[…] images were flatfield corrected with the metamorph software (molecular devices) using background images acquired in empty wells. automated image analysis was performed using the in-house-developed cellcognition software and nuclei and sets of mitotic chromosomes were segmented by local adaptive thresholding. as a quality control for rnai efficiency and specificity, supervised classification […]


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CellCognition institution(s)
Institute of Biochemistry, Swiss Federal Institute of Technology Zurich, Zurich, Switzerland

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