Our objective is to make life easier for multidisciplinary teams who have to deal with very large images (big image data).

More specifically, the CYTOMINE project (started in 2010) is continuously developing a rich internet application using modern web technologies, databases, and machine learning to foster active and distributed collaboration and ease large-scale image exploitation. Our software is e.g. being used by life scientists to help them better evaluate drug treatments or understand biological processes directly from whole-slide tissue images, by pathologists to share and ease their diagnosis, and by teachers and students for pathology training purposes.

Although our initial focus was on biomedical research in cytology and histology whole-slide images, we are developing a generic software that is useful for other types of high-dimensional imaging data from various fields (e.g. botany, geology, astronomy, environmental biology, ...). To ease its reuse in any context, Cytomine is open-source.

If you are looking for collaborators in image-based projects (not restricted to biomedical research), please contact us.

In close collaboration with various researchers, we used our web-based software platform and image recognition algorithms for various biomedical projects. At the end of 2015, our platform was hosting tens of thousands of images for more than one hundred users within our GIGA research center and beyond.

(Sept 2016) We are involved in the NEUBIAS COST Action project for bioimage analysis. If you are interested to come and visit us to learn and integrate Cytomine into your project, please consider to apply for mobility grants for short-term scientific missions.

(May 2016) Thanks to Regional-IT, Daily Science, and Le 15e jour for press coverage of our project and open-source release party.

(Jan. 2016) Our Cytomine paper is formally accepted for publication in Bioinformatics journal.
Cytomine is now released under an open-source software license and available on Github (see instructions below).
You can still request an account on our demo server.

(Jun. 2015) Cytomine has been chosen by the Breast International Group (BIG) for its AURORA program. AURORA is a large, multinational, collaborative metastatic breast cancer molecular screening program that will characterize through next generation sequencing and other techniques the primary tumors and metastatic lesions of 1300 patients, and will follow these patients for up to 10 years. This will allow the enrolment of patients in innovative clinical trials for targeted agents, and a vast improvement of the understanding of metastatic breast cancer.

  (Oct. 2014) The HISTOWEB project (October 2014-2017, funded by Wallonia) is extending the platform for teaching purposes. A preliminary implementation is already accessible for 4000 students at the University of Liege.

(Sept. 2014) A vulgarization of some our research is available on University of Liege Reflexions website

(Oct. 2010) Cytomine kick-off.

Get the source code

Cytomine is released under an open-source license that allow any individual to install, inspect, and extend the application. It is available on Github. Follow our installation instructions (on Linux Ubuntu).

When using our software, you agree to cite our website url (www.cytomine.be) and publications in all your related work (publications, studies, oral presentations). In particular, you agree to cite our (Marée et al., Bioinformatics 2016) paper and to use our logo when appropriate



A documentation wiki is available which includes guides for administrators, developers, and end-users (in particular see our Cytomine User guide).


Cytomine 1.0 was primarily developed at the University of Liege, Systems and Modeling group (Montefiore Institute and GIGA-Research).
Contributors: Raphael Maree (2010-ongoing) initiated and coordinated the work. Loic Rollus (2010-2015), Benjamin Stevens (2010-2014), and Raphael Maree contributed to the general design and functional definition of the software. Loic Rollus, Benjamin Stevens, and Renaud Hoyoux (2014-ongoing) carried out most of the Core, IMS, and WebUI software programming work, while Benjamin Stevens, Gilles Louppe (2013), Loic Rollus, Raphael Maree, Jean-Michel Begon (2014), Remy Vandaele (2014-ongoing) contributed to the implementation of the analysis modules. Philipp Kainz (2014-2015) developed the inter-observer study module (Cytomine-IRIS). Raphael Maree, Pierre Geurts, Loic Rollus, Remy Vandaele, and Louis Wehenkel analyzed data of the empirical studies of image recognition algorithms. Extensions for teaching purposes are coordinated by Gregoire Vincke (2014-...). We thank Pierre Ansen, Julien Confetti, and Olivier Caubo for various other code contributions. We are also strongly relying on other open-source libraries (see documentation). We thank our collaborators (see papers) for their feedback that helped us to shape the software.

How to contribute ?

If you are interested to contribute to Cytomine, please see our documentation for developers, GitHub issues, and feel free to contact us to discuss about your project.

If you want to visit our team to learn more about Cytomine, please contact us to organize a research visit. There are mobility grants for short-term scientific missions through the NEUBIAS COST Action project.

Please check our Cytomine user guide to get access information on our demo server using default accounts.

To request more information or a personal demo account, to suggest ideas, or to discuss about potential collaborations, please contact us.