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!
Thanks! Indeed, digital pathology, satellite imaging and geospatial data share a lot of computational problems: efficient storage, fast spatial retrieval/indexing. I think this could be doable.
As for digital pathology, the field is very much tied to scanner-vendor proprietary formats (SVS, NDPI, MRXS, etc).
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).
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!
When WSI are stored on-premise, they are typically stored on hard drives with a filesystem. If you have a filesystem, you can use OpenSlide, and use a viewer like OpenSeaDragon to visualize the slide.
WSIStreamer is relevant for storage systems without a filesystem. In this case, OpenSlide cannot work (it needs to seek and open the file).
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/
Thanks! Indeed, digital pathology, satellite imaging and geospatial data share a lot of computational problems: efficient storage, fast spatial retrieval/indexing. I think this could be doable.
As for digital pathology, the field is very much tied to scanner-vendor proprietary formats (SVS, NDPI, MRXS, etc).
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).
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.
Or IIIF.
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!
When WSI are stored on-premise, they are typically stored on hard drives with a filesystem. If you have a filesystem, you can use OpenSlide, and use a viewer like OpenSeaDragon to visualize the slide.
WSIStreamer is relevant for storage systems without a filesystem. In this case, OpenSlide cannot work (it needs to seek and open the file).
How does this handle images with different compression formats?
hey, I need this