Features Solution Center

Upload high-dimensional images in various formats. Cytomine natively supports 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 converts them into fast pyramidal image formats.

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 user-defined domain-specific terms), and associate meta-data.

Explore your high-resolution (multi-gigapixel) image from anywhere in the world at multiple resolutions using modern navigation interfaces. Through distributed image tiling, image sizes are not limited to your computer memory.

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.

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

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

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 you to correct algorithms and derive relevant final quantification results.

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 in). Cytomine is open-source hence fully extensible.

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