TCGA-LIHC slide images.

[Dr Barkha GUPTA]

Hello ,

I wanted to interpret 'Tissue Images' of "Hepatocellular Carcinoma from TCGA Pan cancer Atlas", precisely, TCGA-LIHC H&E slide images.

 

I have two questions in this regard:-

1) We are only able to access 50 odd images from www.cbioportal.org website. Earlier we used to have access to more than 350 cases.

2) We are not able to switch to the full screen mode to view the image. Currently the' toggle full page' switch present is not functioning properly.

Also, I tried to download these slides from Repository but there is a message saying that they are currently not available for download.

It would be very helpful if you could please look into this matter at the earliest.

Thanks & Regards,

 

--
Dr BARKHA GUPTA, MD
Research Pathologist

INSERM UMRS 1138-équipe 28
Premier étage, Escalier A
Centre de Recherche des Cordeliers
15 rue de l'école de médecine
75006 Paris

France

[Tali Mazor]

Hi Barkha,

The slides images that you see through cBioPortal are actually an embedding of the Cancer Digital Slide Archive website (https://cancer.digitalslidearchive.org/). I suggest reaching out to them about the cases that are no longer available, as well as with any questions about downloading the images.

I do see that the full screen function is working if you view a slide directly on the CDSA website, but is not working within cBioPortal. I've created a ticket where you can track our progress on resolving the full screen issue: https://github.com/cBioPortal/cbioportal/issues/8685. While we work to resolve it, you can always pull up the images directly on the CDSA website and make them full screen there.

-Tali

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[Aaron Lisman]

Hi Barkha, 

I would second Tali's suggestion that you try to find the images directly on the CDSA website.  If you find something available there that is NOT available on cBioportal, please let us know.   

As for full screen mode, I'm curious, did functionality ever work for you (in context of cBioPortal)?  

--Aaron

To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/CAGc5ufTUB9yAw8v%2B%3DSvUYst414RW5Kqn0ugOwvdoogFOaOsacQ%40mail.gmail.com.

[Dr Barkha GUPTA]

Hello Tali,

Thank you very much for your reply.

I have written to CDSA also via email as you have suggested.

Do you know of other ways to access the TCGA-LIHC slides?

Also, when would it be possible to download the slide images from TCGA  repository?

Currently, there is a popup saying the download is not possible.

Regards,

Barkha

 

--
Dr BARKHA GUPTA, MD
Research Pathologist

INSERM UMRS 1138-équipe 28
Premier étage, Escalier A
Centre de Recherche des Cordeliers
15 rue de l'école de médecine
75006 Paris

France

[Nikolaus Schultz]

Hi,

I think the NCI has temporarily suspended all histology image downloads. We do not have a copy of the images, and have no additional information on when they will become available again.

Niki.

To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/5256017656d6c34535db235d57248122%40inserm.fr.

[Dr Barkha GUPTA]

Hello everyone,

Thank you all for your replies.

I wrote to CDSA on 'dagu...@gmail.com' two days ago but I have not received any reply yet.

Do anyone of you also know of any alternate contact email id?

I appreciate your help.

Cordially,

Barkha

--
Dr BARKHA GUPTA, MD
Research Pathologist

INSERM UMRS 1138-équipe 28
Premier étage, Escalier A
Centre de Recherche des Cordeliers
15 rue de l'école de médecine
75006 Paris

France

[Tali Mazor]

Hi Barkha,

That's the only contact I know of for CDSA. Sorry I can't be of more help.

-Tali