Intro to Cytomine 2: Cytomine & BIAFLOWS for data and computer scientists [NEUBIAS Academy Webinar]
Channel: NEUBIAS
Date: 29/05/2021

This is the 2nd chapter of a 2-webinars series on the Cytomine environment for collaborative annotation on the web, image analysis and benchmarking.In this second session we cover more advanced features for collaborative image analysis over the web with Cytomine (https://cytomine.org) & Biaflows (https://biaflows.neubias.org):


– Overview of existing image processing/AI modules (e.g. sample detection, tumor delineation, cell segmentation, …)

– Interoperability: Cytomine API (web services) & Java/Python clients for importing/exporting/sharing multidimensional and multimodal data
– Integration and application of external algorithms using containers (Docker/Singularity) for reproducibility
– Benchmarking using BIAFLOWS server


=========  LEARNING OUTCOMES

After this session you will be able to:– Apply advanced algorithms (AI or not) using Cytomine Web user interface and Python/Java clients
– Integrate your own code using containers and descriptors for reproducibility and make them available on the web
– Interoperate with Cytomine using its web API and Python/Java clients to import/export/share data

– Use Biaflows web server for benchmarking algorithms


========= SPEAKERS

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).

Sébastien Tosi (PhD in signal processing, 2007) is BioImage Analyst at IRB Barcelona where he supports a large community of scientists and develops hardware and software tools (e.g. LOBSTER, MosaicExplorerJ, AutoScanJ. He leads the BIAFLOWS project, together with members of Workgroup 5 in NEUBIAS.



Moderators: Elnaz Fazeli (UTurku), Mafalda Sousa (i3S Porto), Renaud Hoyoux (Cytomine), Ulysse Rubens and Romain Mormont (Univ. Liège), Rocco d'Antuono (Francis Crick Institute).



======== Question and Answers

They will soon be available on https://forum.image.sc/