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Analysing gigapixel images online is possible with Cytomine

(Last Updated On: 4 June, 2018)

We have a collaborating project between Norway, Moldova, Armenia and Belarus in Oral Pathology. In order to view slides online we installed a software called Cytomine. This software, or multiple combined software/applications, is developed in Belgium by a cooperating team. All about Cytomine can be read here: https://cytomine.coop/

This is an open source software. It is installed on a Linux Ubuntu 16.04 LTE server with Docker CE. The server has 96GB memory, 2TB storage and 24 VCPU’s. It is located in University of Bergen, hosted by the UH-Iaas project group (http://iaas.readthedocs.io/en/latest/getting_started/index.html)

This application gives the user to view slides (pictures) of multiple gigabyte online and almost without any download time. For instance we have tested it with a 5GB large slide, and it could be viewed immidiately online through a 4G mobile phone in Yerevan, Armenia through the Internet with the servers located in Norway, Bergen.

The Cytomine software can be used by students, teachers, pathologist for viewing, annotating, discussing tissue slides (or any picture actually).

Our server is located here:

https://cytomine-core.app.uib.no

In order to install Cytomine you need to have a basic understanding of Linux Ubuntu, bash scripting, Docker and general web-server technology.

I have created a short video that shows how the software works:

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