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  • Upload

    Upload high-dimensional images in various formats. Cytomine supports natively various digital pathology and microscopy formats (TIFF, Generic tiled TIFF, Aperio SVS, Hamamatsu VMS and NDPI, 3DHistech MRXS, Leica SCN, Philips TIFF, OME-TIFF, ...) or convert them in fast pyramidal image formats.

    Category:
    • Image management

    Availability: Out of the box

    Licence: Apache 2.0

  • Organize

    Organize your images into projects (or "picture folders") where each project corresponds to a specific study or experiment. Easily manage authenticated users with permission rights, define ontologies (with domain-specific, user-defined, vocabulary terms), and associate meta-data.

    Category:
    • Project management

    Licence: Apache 2.0

  • Explore

    Explore your high-resolution (multi-gigapixel) image sequences (x,y,z,c,t) from anywhere in the world at multiple resolutions using modern navigation interfaces inspired by web-based geographic applications. Through distributed image tiling, image sizes are not limited to your computer memory.

    Category:
    • Image visualisation

    Licence: Apache 2.0

  • Annotate

    Annotate your images semantically by drawing multiple regions of interest (ellipses, rectangles, polygons, freehand drawings) and describe them through user-defined terms from structured vocabularies (ontologies), key-value properties, or metadata. Take advantage of our content-based image retrieval algorithms to speed up annotation.

    Category:
    • Image analysis
    • Semantic information

    Licence: Apache 2.0

  • Consolidate

    Consolidate image atlases (ground truths) and share them or use them as input of machine learning algorithms.

    Licence: Apache 2.0

  • Share and Review

    Share and Review images and their semantic annotations with your collaborators worldwide using simple URLs. Our e-mailing and communication mechanisms allow to discuss cases with your colleagues and follow other user's observation paths in real-time through the Internet, hence facilitating second opinion requests and improving interobserver agreement and reproducibility.

    Category:
    • Image management

    Licence: Apache 2.0

  • Analyse

    Analyze your sets of images with our generic, tree-based, machine learning algorithms implemented on modern, multi-core architectures and computing clusters. Algorithms for the recognition of tissue substructures, cell types, and landmarks can be trained by experts to speed-up and refine the detection and quantification of the most relevant biological "objects" in your images. Proofreading web user interfaces allow to correct algorithms and derive relevant final quantification results.

    Category:
    • Image analysis

    Availability: Out of the box

    Licence: Apache 2.0

  • Extend

    Extend the software with your own algorithms, plug-ins, web applications. Interoperate from your third-party software communicating through our RESTful standardized programming interfaces (Java and Python clients are already available, other languages can be easily plugged). Cytomine is open-source hence fully extensible.

    Licence: Apache 2.0

  • LTI

    The Learning Tools Interoperability protocol synchronises users and their activities between the Cytomine software and Learning Managing Systems such as Moodle, Claroline Connect, Open Edx or BlackBoard.

    Category:
    • User management

    Availability: On demand

    Licence: Cytomine.coop