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hubmapconsortium / portal-ui

HuBMAP Data Portal front end
https://portal.hubmapconsortium.org
MIT License
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Visualization for clinical imagining #2616

Open mccalluc opened 2 years ago

mccalluc commented 2 years ago

The directory schema isn't finalized, but we may receive DICOM, TIFF, or AVI (assay description in progress).

There is no pipeline currently:

Ivan Cao-Berg 11:42 AM Matt Ruffalo just to confirm, there are no processing pipelines for clinical data (CT, ultrasound and MRI) at the moment?

Matt Ruffalo 11:42 AM Ivan Cao-Berg that's correct

We probably need a visualization-only pipeline. My sense is that these assays are not high-resolution: So superficially similar to the pyramid building, but it might just be a question of image translation.... but if there are multiple images in the dataset, not sure what we're supposed to do with them.

ilan-gold commented 2 years ago

@mccalluc I'm adding here what I said on slack:

We can handle the data once loaded (to some degree).  Loading it might be challenging, at least for DICOM if we keep it in the DICOM format.  We’ll need a new loader assuming it’s possible (gotta assume so given the number of visualization tools out there).  As for rendering, this needs to be assessed as to how deep we want to go.  Medical imaging has its vocabulary for how you control the image rendering settings from what I can tell, some sort of click and drag combination.  This is of course different than what we have right now.  We should probably talk to an expert about this.  I’m not even sure we want this in Vitessce.  Alternatively we can just use sliders but I have never seen them for controlling rendering settings on e.g MRI images

So to be clear there are a few threads here:

  1. Do we want to support natively reading DICOM? If we do, what is the timeline needed? Can we meet it?
  2. Do we want to convert DICOM to OME-TIFF? If so, who is going to tackle this?
  3. Do we want special rendering available for medical images? If so, should we build this into vitessce?
ilan-gold commented 2 years ago

@ngehlenborg brings up a good idea - just using a DICOM viewer!