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Digital pathology using the DICOM service

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Pathology is a branch of medical science primarily concerning the cause, origin, and nature of disease. It involves the examination of tissues, organs, bodily fluids, and autopsies in order to study and diagnose disease.

Historically, biopsies of tissues are stored in glass slides and investigated under microscope. This creates challenges when clinicians and pathologists need to share information for consultations and diagnosis as well as for research.

Digital imaging is becoming increasingly popular in the field of pathology as a way to support sharing images outside the lab, training AI/ML models, and for long term storage. This transformation is fueled by the commercial availability of instruments for digitizing microscope slides.

Today, digital pathology scanners generally output imaging into proprietary formats. This complicates sharing and AI/ML model training, blunting many of the advantages of digitization. To ease this transformation, many organizations are beginning to convert Whole Slide Imaging (WSI) digital slides to DICOM-standard format. Once these images are in DICOM® format, these images can be stored in commercially available PACS systems, where they can be managed using tools and processes that have been perfected over decades by radiologists.

DICOM service for digital pathology

The DICOM service supports unique digital pathology requirements like:

  1. Scale and performance needed to upload pathology DICOM instances that are multiple GBs in size.
  2. Fast frame access to allow the web viewer to pan and zoom DICOM pathology images smoothly with no lags or blurriness.
  3. A cost-effective way to store images long-term post diagnosis for archival and research use.

Diagram showing whole-slide imaging digitization and cloud storage.

Digitization

Although the DICOM standard now supports whole-slide images (WSI), many acquisition scanners don't capture images in the DICOM format. The DICOM service only supports images in the DICOM format, therefore a format conversion is required for WSI in other formats. Several commercial and open-source solutions exist to perform these format conversions.

Here are some samples open source tools to build your own converter:

Storage

Each converted WSI results in a DICOM series with multiple instances.

Batch upload

Considering the bigger size and number of instances that needs to be uploaded, we recommend batch upload of each series or a batch of converted WSIs using Import

Streaming upload

If you want to upload each file as they get converted you can use the STOW single part request like below.

Prerequisites

curl -X POST \
    -H "Content-Type: application/dicom" \
    -H "Authorization: Bearer {token}" \
    -H "Accept: application/dicom+json" \
{service-url}/{version}/studies \
    --data-binary {dcmFile}.dcm

We have tested supporting tens of GBs upload in few seconds.

Retrieval

Viewers retrieve tiles that are stored as frames in a DICOM instance. Each DICOM instance can contain multiple frames. We recommend using parallel single part GET frame for better performance.

Prerequisites

curl -X GET \
    -H "Authorization: Bearer {token}" \
    -H "Accept: application/octet-stream; transfer-syntax=*" \
{service-url}/{version}/studies/{studyInstanceUid}/series/{seriesInstanceUid}/instances/{sopInstanceUid}/frames/{frameNumber} \
    --output {fileName}

We have tested supporting download of 60Kb tile in around 60-70ms from client.

Viewers

We recommend using any WSI Viewer that can be configured with a DICOMWeb service and OIDC Authentication.

Sample open-source viewer

Follow the CORS guidelines if the Viewer directly interacts with the DICOM service

Find an ISV partner

Reach out to dicom-support@microsoft.com if you want to work with our partner ISVs that provide end-to-end solutions and support.

Next steps

Deploy the DICOM service in Azure

Use DICOMweb APIs with the DICOM service

Note

DICOM® is the registered trademark of the National Electrical Manufacturers Association for its Standards publications relating to digital communications of medical information.