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README.md

DSA MONAILabel extension

Requirement

You need to install DSA and upload some test images.

Refer: https://github.com/DigitalSlideArchive/digital_slide_archive/tree/master/devops/dsa

Installation

You can use projectmonai/monailabel-dsa:latest plugin from dockerhub. Otherwise you can build from sources as follows.

  cd plugins/dsa
  docker build -t projectmonai/monailabel-dsa:latest .

You can pass the default MONAILabel server by defining following environment variable in docker compose for DSA. This will also help to pre-fetch the available models from MONAILabel server.

---
version: '3'
services:
  girder:
    environment:
      SLICER_CLI_WEB_MONAI_LABEL_SERVER: http://monai.label.com:8000

Upload new Task (under Slicer CLI Web Tasks) using the above docker image. This will add/enable MONAILabel under Analysis Page.

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NOTE:: Provide additional options like dsa_api_key and dsa_asset_store_path while running the MONAILabel server for faster resource sharing between MONAILabel and DSA.

MONAILabel Server configs for DSA

Following are some config options:

Name Description
preload Preload models into GPU. Default is False.
roi_size Default ROI Size for inference in [x,y] format. Default is [1024,1024].
dsa_folder Optional. Comma seperated DSA Folder IDs. Normally it is <folder_id> of a folder under Collections where Images are stored.
dsa_api_key Optional. API Key helps to query asset store to fetch direct local path for WSI Images.
dsa_asset_store_path Optional. It is the DSA assetstore path that can be shared with MONAI Label server to directly read WSI Images. 
  # run server (Example: DSA API URL is http://0.0.0.0:8080/api/v1)
  ./monailabel/scripts/monailabel start_server --app sample-apps/pathology \
    --studies http://0.0.0.0:8080/api/v1 \

  # run server (Advanced options)
  ./monailabel/scripts/monailabel start_server --app sample-apps/pathology \
    --studies http://0.0.0.0:8080/api/v1 \
    --conf dsa_folder 621e94e2b6881a7a4bef5170 \
    --conf dsa_api_key OJDE9hjuOIS6R8oEqhnVYHUpRpk18NfJABMt36dJ \
    --conf dsa_asset_store_path digital_slide_archive/devops/dsa/assetstore

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