Introduction to Cytomine: Collaborative Web Annotation -- [NEUBIAS Academy@Home] Webinar
Channel: NEUBIAS
Date: 2021-05-07

This is the 1st chapter of a 2-webinars series on the Cytomine environment for collaborative annotation on the web, image analysis and benchmarking. (https://cytomine.org)



In this first session we will present an overview of Cytomine (https://cytomine.org) main features & concepts for collaborative image analysis over the web:

– Organization of imaging datasets into projects with access rights and user roles, upload of images.
– Remote visualization of very large images (digital pathology, multidimensional, hyperspectral), synchronized viewer, multiple views, …

– Creating and sharing metadata and annotations: manual annotations of regions of interests (incl. point, polygon & freehand tools), user layers, ontology terms, properties, description, tags, attached file, annotation links.

– Configuration & settings of a Cytomine instance and projects (custom user interface, …).

– Application of algorithms using the web interface for semi-automated annotations (overview, to be followed in Session 2)



=========  LEARNING OUTCOMES
After this session you will be able to:

– Use Cytomine to remotely visualize and share large images (digital pathology & other fields)
– Create very rich manual annotations of your images (e.g. to create ground-truths for machine learning, pathology atlases, …)

– Apply machine learning routines directly on the web (to be further detailed in Session 2)



========= SPEAKERS

Grégoire Vincke (Msc. In Veterinary Sciences and in Higher Pedagogy) is co-founder and CEO at Cytomine Cooperative and co-founder and CMBDO at Cytomine Corporation. Since 2014 he is training physicians, teachers, students, and researchers to use the Cytomine collaborative platform for biomedical image analysis.

Raphaël Marée (PhD in machine learning, 2005) initiated the development of the collaborative Cytomine web software in 2010 and he is now head of Cytomine Research & Development at the University of Liège (https://uliege.cytomine.org).

Moderators: Renaud Hoyoux (Cytomine), Ulysse Rubens and Romain Mormont (Univ. Liège), Rocco d'Antuono (Francis Crick Institute), Julien Colombelli (IRB Barcelona).


======== Question and Answers
They will soon be available on https://forum.image.sc/ 



======== Material

The slides presented in this webinar are available here:https://people.montefiore.uliege.be/maree/cytomine/Cytomine_NeubiasAcademy_part1.pdf