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Secure viewing of tissue slides from cBioPortal patient view

cBioPortal is an open source web application for exploring genomic datasets. It makes it really easy to query for specific mutations, mutated genes, overexpression, deletions or amplifications of genes (and more) and to quickly compare these samples with the rest using Kaplan-Meier survival curve.

cBioPortal has multiple public servers (for example https://www.cbioportal.org or https://www.cbioportal.org/genie/) that host publicly accesible datasets from published studies, but it's also increasingly popular to run private cBioPortal servers that host confidential datasets or studies that are still in progress within institutions or as a hosted service (for example by Health-RI).

cBioPortal has now for a while supported viewing public slides from the TCGA datasets and from the internal slide viewer used at MSKCC (where cBioPortal was created) but from version 3.6 it's also possible to link your slides in other platforms. We were excited by the new possibilities and started working on supporting it securely.

What cBioPortal does is not just showing a link to the slide but inserting (the technical term is embedding) the whole slide viewer within the page that shows patient and sample details. If hackers could embed any website on a page they control, they might be able to steal information so secure web applications often completely disable it. Slide Score was no exception, so we had to design a way to allow this without compromising security. Embedding is now possible but only under certain conditions, from known good web applications and addresses and with limited functionality. This will ensure that your research data is safe.

How to get your slides in cBioPortal? Slide Score users who can download results or access study administration will see a new button Export List when viewing details of a study. This will show a dialog that allows copying a list of all slide or case names in the study and their corresponding embedding link. These links can be imported in cBioPortal as a "resource" linked to a sample or patient. Sample or patient view in cBioPortal will then show a new tab that contains a basic Slide Score viewer and a link to open the slide in Slide Score to be able to score it and access all other functionality.

Would you like to securely include your slides from a private cBioPortal server? Contact us!

Slide Score whole slide images in cBioPortal