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RationAI Enhanced WSI Service by Empaia

IDrationai-wsi-tile-source
Version0.1.0
Sourcemodules/rationai-wsi-tile-source

Used by​

Documentation​

Standalone WSI Service​

Implementation of OpenSeadragon Tile Source access to the standalone WSI service.

Modified by RationAI, the WSI service can read proprietary WSI file formats in the standalone mode, accessing WSIs by their IDs (dependent on the mapper usage).

Also supports multifile access on the API extension /files.

Usage​

Configure the default viewer ENV using the named slide-protocol registry. The template is a backtick expression with data (scalar DataID) in scope; the server URL is embedded directly in the template.

   "slide_protocols": {
       "empaia_standalone": "`{\"url\": \"http://localhost:8080/v3/files/info?paths=${data}\", \"type\": \"empaia-standalone\"}`"
   },
   "default_background_protocol":    "empaia_standalone",
   "default_visualization_protocol": "empaia_standalone"

or reference the registered name from a session via BackgroundItem.protocol / DataOverride.protocol.

You can also just set an URL to the WSI server, for example:

   "slide_protocols": {
       "wsi_batch": "`http://localhost:8080/v3/batch/info?slides=${data}`"
   },
   "default_background_protocol":    "wsi_batch",
   "default_visualization_protocol": "wsi_batch"

But this approach has its limitations.

The legacy image_group_server + image_group_protocol + data_group_* fields are still accepted and auto-synthesized into deprecated registry entries (with a one-shot console warning), but new deployments should use the shape above.

Options​

Options include: format - one of jpeg, png, tiff, bmp, gif. If omitted, non-RGB/RGBA slides default to tiff. quality - for e.g. jpeg the image quality to request. channels - if format is tiff, the channels to request (array of indexes) or all literal. If omitted, all channels are requested by default. plugin - name of the WSI-Service slide-reader plugin to use (e.g. openslide, tifffile, wsidicom). When omitted, the server auto-detects. Forwarded as the plugin query parameter on tile, thumbnail, label, and ICC-profile requests. To also influence the initial slide-info fetch, embed plugin=… directly in the slide_protocols URL template — setSourceOptions runs after info has been fetched.

You can set these options per data entry via DataOverride.options:

"data": [
  {
    "dataID": "slide.tiff",
    "options": { "plugin": "tifffile", "format": "tiff", "channels": "all" }
  }
]