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Show HN: Streaming gigabyte medical images from S3 without downloading them

Show HN: Streaming gigabyte medical images from S3 without downloading them

el_pa_b

Comments (46)

  • tomnicholas1
    The generalized form of this range-request-based streaming approach looks something like my project VirtualiZarr [0].Many of these scientific file formats (HDF5, netCDF, TIFF/COG, FITS, GRIB, JPEG and more) are essentially just contiguous multidimensional array(/"tensor") chunks embedded alongside metadata about what's in the chunks. Efficiently fetching these from object storage is just about efficiently fetching the metadata up front so you know where the chunks you want are [1].The data model of Zarr [2] generalizes this pattern pretty well, so that when backed by Icechunk [3], you can store a "datacube" of "virtual chunk references" that point at chunks anywhere inside the original files on S3.This allows you to stream data out as fast as the S3 network connection allows [4], and then you're free to pull that directly, or build tile servers on top of it [5].In the Pangeo project and at Earthmover we do all this for Weather and Climate science data. But the underlying OSS stack is domain-agnostic, so works for all sorts of multidimensional array data, and VirtualiZarr has a plugin system for parsing different scientific file formats.I would love to see if someone could create a virtual Zarr store pointing at this WSI data![0]: https://virtualizarr.readthedocs.io/en/stable/[1]: https://earthmover.io/blog/fundamentals-what-is-cloud-optimi...[2]: https://earthmover.io/blog/what-is-zarr[3]: https://earthmover.io/blog/icechunk-1-0-production-grade-clo...[4]: https://earthmover.io/blog/i-o-maxing-tensors-in-the-cloud[5]: https://earthmover.io/blog/announcing-flux
  • carderne
    I did something similar once for a mining technique called “core logging”. It’s a single photo about 1000 pixels wide and several million “deep”: what the earth looks like for a few km down.Existing solutions are all complicated and clunky, I put something together with S3 and bastardised CoGeoTIFF, instant view of any part of the image.Wish I knew how to commercialise it…
  • rwmj
    https://dicom.nema.org/dicom/dicomwsi/Interesting guide to the Whole Slide Images (WSI) format. The surprising thing for me is that compression is used, and they note does not affect use in diagnostics.Back in the day we used TIFF for a similar application (X-ray detector images).
  • matthberg
    Seems very similar to how maps work on the web these days, in particular protomap files [0]. I wonder if you could view the medical images in leaflet or another frontend map library with the addition of a shim layer? Cool work!0: https://protomaps.com/
  • mlhpdx
    A while back I worked on a project where s3 held giant zip files containing zip files (turtles all the way down) and also made good use of range requests. I came up with seekable-s3-stream[1] to generalize working with them via an idiomatic C# stream.[1] https://github.com/mlhpdx/seekable-s3-stream
  • tokyovigilante
    This is really a job for JPEG-XL, which supports decode of portions of larger images and has recently been added to the DICOM standard.
  • Sleaker
    Maybe a bit pedantic, but if you're streaming it, then you're still downloading portions of it, yah? Just not persisting the whole thing locally before viewing it.Edit: Looks like this is a slight discrepancy between the HN title and the GitHub description.
  • lametti
    Interesting - I'm not so familiar with S3 but I wonder if this would work for WSI stored on-premises. Imposing lower network requirememts and a lightweight web viewer is very advantageous in this use case. I'll have to try it out!
  • invaderJ1m
    How does this compare to things like COGs (Cloud Optimised GeoTIFFs) or other binary blob + index raster pyramid formats?Was there a requirement to work with these formats directly without converting?
  • yread
    You could probably do it completely clientside. I have a parser for 12 scanner formats in js. It doesnt read the pixels, just parses metadata but jpeg is easy and most common anyway
  • Nora23
    How does this handle images with different compression formats?
  • isuckatcoding
    Is there a visual demo of this?
  • andrewstuart
    Please don’t use AWS S3 there’s vast numbers of much cheaper compatible choices.
  • huflungdung
    [dead]
  • tonyhart7
    hey, I need this
  • tonymet
    If only we had NFS to begin with