Download images in cancer slide archive

Now we have the 1, files that we would like to download. I cannot create a user. Would you help me? If you would like access to their site, I would suggest emailing them. What I really want is access to the reports for processing with natural language. Would you have a dataset that you know that provides something like this? Hi Andrew, many thanks for this. I am interested in playing around with DL methods and have couple of questions. How do you convert svs files to tiff or any other format?

Which image format do you prefer to work with? How do you tile the images and how many tiles do you create? Is that correct? Later they found out that there are not much needs to keep 3 sections, and scaled down to only 2.

The magnification is stored in the metadata which you can pull out using e. I was wondering if you had already tried to correlate finding of pathology and radiology on the image data from TCGA? Whether for pathology the images are well annotated and using the ID you can link the finding of the diagnostic slides to the associated clinical data, on the radiology we are having some troubles.

Very often there are multiple visits for a patient hence multiple series and for each visit dates are randomized so we do not know which is the diagnostic visit. If you have tried to link the pathology to the radiology and can give us some hints that would be greatly appreciated.

Thanks for your question. Yeah indeed it is very interesting but also challenging for a lot reasons. We will keep digging on the online data from TCGA …. Any help would be much appreciated!

I would be very careful and not make that assumption without visual verification. This tool we built helps to address to find these slides and those with artifacts. What is your opinion on doing that? I would avoid at all costs unless the particular experimental design calls for it. Ultimately flash-frozen tissue has a significantly different presentation due to tissue damage imparted during the freezing process. Thank you! Sorry, no idea. Keep in mind some of the files may not be available unless you have an authorized GDC account.

SVS files can also be downloaded. A good case set to use to familiarize yourself with the site is the melanoma collection. Mostly in French. The Iowa Virtual Slidebox.

Access: Free Access; No login or membership required Viewer: Biolucida viewer Additional Comments: Over histopathology slides, organized and tagged. Well organized. Access: Free Access; Login required Viewer: Web-Based; OpenLayers, with static tiled images created from JP2 files; Mac or PC Organization: Cases arranged by body system, with brief history and diagnosis Additional Comments: Weekly unknowns from since , with dermatopathology representing more than half of the loaded cases.

Predominantly adult cases. Access: Free Access but registration required. May take several days to activate.

Viewer: Mac or PC with build in viewer; no plugins required. Organization: Neuropathology teaching site, with a mixture of instructional video, static images with special stains, and region-of-interest histology. Additional Comments: Some of the histologic images are whole slide images focusing on a regions of interest, rather than the entire glass slide.

Annotations, which can be turned on and off, describe the various morphologic features. Many of the images are static. There is abundant use of special stains. Excellent site for learning neuropathology. Additional Comments: Good collection of pathology cases. Also excellent set of seminar cases. Diagnoses provided. Seamless image rendering for smooth and clear navigation.

A review of essential dermatopathology terms. Touch enabled highlights of key findings for each term. Board relevant cases offered in a timed exam format. Random test generator makes each exam a new challenge. Mobile devices do not require a plugin.