Add DICOM, NDPI, document Hamamastu format

[hexylena]

Support for the DICOM medical imaging format.

How to test the changes?

(Select all options that apply)

• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
• Instructions for manual testing are as follows:
  1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

• I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

[nsoranzo]

(I know it's in Draft, but) missing to add changes to lib/galaxy/config/sample/datatypes_conf.xml.sample ?

[bgruening]

Is that still draft @hexylena ?

[hexylena]

Yes, it is still intentionally in draft.

[kostrykin]

Do you plan to continue working on this? @hexylena
Were there any major blockers that you encountered?

[hexylena]

Hi @kostrykin unfortunately I left that position. I was hoping a colleague might take over this PR but that will not happen.

There are no major blockers, I think the only open question was "how much metadata is necessary to write useful tools", since some dicom are going to be single images, or slices, or pyramids, I suspect that will be an important aspect, but imaging is very far away from my areas of expertise, so, input from actual end users would be helpful.

Nevertheless, I've left that position, and the associated grant has ended, so, this is all that could be done during that time. I left it open in case the community wants to take it over, but until the metadata question is resolved, I chose to leave it in draft.

Happy to add any necessary persons to my fork to contribute to this.

[nsoranzo]

Closing in favour of #21385 .
Thanks @hexylena for starting this!

[hexylena]

Since it was closed without picking up the NDPI, hamamastu changes I've changed the title to reflect that, maybe someone else will pick those up later, one can hope.