Add QuPath viewing notebook

[melissalinkert]

In a similar spirit as #67, this adds a notebook that walks through the basics of how to use QuPath to open WSI data, in particular DICOM and converted OME-TIFF.

There is no code in this notebook, it is only text, images, and video. The videos were too large to embed, so are separate files that are referenced within the notebook. If something other than a notebook would be more useful to represent this information, I can certainly switch to markdown or something else.

Note that if viewing the notebook directly in GitHub, it may not display correctly. Checking out this pull request's branch and running the notebook should work as intended.

cc @fedorov, @dclunie, @erindiel

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[DanielaSchacherer]

Hi Melissa,

I am Daniela, also part of the IDC team and Andrey asked me to check out your notebook and let you know my feedback!
I think, this notebook is very helpful for users that are interested in IDC data, but are loyal users of QuPath and don't want to switch tools or just do some of their normal stuff they use to do with QuPath on IDC data. As you said yourself, this could maybe - instead of a notebook - be presented in a different form and I thought about a subpage in IDC documentation or a folder in Github with a README and your videos. But I am not sure, if it is worth the effort right now or we can just stay with the notebook. For some reason, in Github, I can not display the notebook completely and had to download it to see the rest (see attached screenshot). Not sure, if the problem here is on my side or on Github's (see below).
One more thought that I had: it might be nice (as this notebook is for beginners) to go one more step back and refer to documentation on how to download the images in the first place.

[fedorov]

I also think that since this tutorial does not have any code, it is best to maintain it in a dedicated documentation page. Python notebook is suboptimal and unnecessary here, and also putting large video files into the code repository is generally not a good idea. To make it easier for you @melissalinkert I will make a page under IDC docs and transfer the content there. I will then point you to that page and give you instructions how to update the content, if you need to do so.

[melissalinkert]

Thank you for the comments, @DanielaSchacherer and @fedorov.

For some reason, in Github, I can not display the notebook completely and had to download it to see the rest (see attached screenshot). Not sure, if the problem here is on my side or on Github's (see below).

This is unfortunately a general issue with displaying more complex notebooks in Github, and is something @erindiel and I saw when initially looking at this as well.

One more thought that I had: it might be nice (as this notebook is for beginners) to go one more step back and refer to documentation on how to download the images in the first place.

That makes complete sense. Is there an existing page we should link to, or just copy the instructions similar to what is noted in https://github.com/ImagingDataCommons/IDC-Tutorials/pull/67/files#r1744114094?

I also agree that a documentation page instead of a notebook makes sense here. @fedorov, if you would prefer I move the text/videos to a documentation page, I am happy to do so, just let me know where to edit or open a new pull request.

[DanielaSchacherer]

This is unfortunately a general issue with displaying more complex notebooks in Github, and is something @erindiel and I saw when initially looking at this as well.

Ok, another argument for moving this notebook to IDC documentation :)

That makes complete sense. Is there an existing page we should link to, or just copy the instructions similar to what is noted in https://github.com/ImagingDataCommons/IDC-Tutorials/pull/67/files#r1744114094?

I also agree that a documentation page instead of a notebook makes sense here. @fedorov, if you would prefer I move the text/videos to a documentation page, I am happy to do so, just let me know where to edit or open a new pull request.

If it's going to be a page in the IDC documentation, we could just link here in my opinion: https://learn.canceridc.dev/data/downloading-data.

[fedorov]

I now created a dedicated "Tutorials" section in the docs, a subsection dedicated to slide microscopy, and added the content of this notebook there: https://learn.canceridc.dev/tutorials/slide-microscopy/qpath-for-sm-visualization.

To update the content, this is the file to change: https://github.com/ImagingDataCommons/IDC-Docs/blob/prod/tutorials/slide-microscopy/qpath-for-sm-visualization.md.

I placed mp4 files into Google Drive and embedded as Google Slides, since I do not want to commit such large files into a GitHub repo. This is the directory with the content (I can share if you would like to add content).