12.1. Liver Segmentation Pipeline¶
The Liver Segmentation pipeline is one of the reference pipelines provided with Clara Deploy SDK. This pipeline depends on the Clara Deploy DICOM Adapter to receive DICOM images, specifically an axial series of an abdominal CT study. Once the DICOM instances are stored, the pipeline is started to first convert the DICOM instances to a volume image in MetaIO format and then processes the input volume image with the Liver Segmentation AI model. The AI model generates the labeled liver and tumors (within the liver) as a binary mask on slices of the volume of the same size as the input. The liver is labeled as 1, tumors within the liver are labeled as 2, and the background is labeled as 0. In its final steps, the pipeline outputs the binary mask as a new DICOM series using the original study instance UID; also, it outputs the original and segmented volumes to the Clara Deploy Render Server for visualization on the Clara Dashboard.
12.1.1. Pipeline Definition¶
The Liver Segmentation pipeline is defined in the Clara Deploy pipeline definition language. This pipeline utilizes built-in reference containers to construct the following set of operators:
- The dicom-reader operator converts input DICOM data into volume images in mhd format.
- The liver-tumor-segmentation operator performs AI inference against the NVIDIA Triton Inference server to generate liver and tumor segmentation volume images.
- The dicom-writer converts the segmented volume image into DICOM instances with a new series instance UID and the original DICOM study instance UID.
- The register-dicom-output operator registers the DICOM instances with the Clara Deploy DICOM Adapter which in turn stores the instance on external DICOM devices per configuration.
- The register-volume-images-for-rendering operator registers original and segmented volume images with the Clara Deploy Render Server for visualization.
The following is the details of pipeline definition, with comments describing each operator’s functions as well as input and output.
api-version: 0.4.0 name: liver-tumor-pipeline operators: # dicom reader operator # Input: '/input' mapped directly to the input of the pipeline, which is populated by the DICOM Adaptor. # Output:'/output' for saving converted volume image in MHD format to file whose name # is the same as the DICOM series instance ID. - name: dicom-reader description: Converts DICOM instances into MHD, one file per DICOM series. container: image: clara/dicom-reader tag: latest # Use the following variable to configure DICOM Reader to save mhd, nii, or nii.gz # Note the attribute 'variables' should indent should match that of 'container'. #variables: # NVIDIA_CLARA_DCM_TO_FORMAT: nii.gz input: - path: /input output: - path: /output # liver-tumor-segmentation operator # Input: `/input` containing volume image data, MHD format, with a single volume. # Output: `/output` containing segmented volume image, MHD format. # `/publish` containing original and segmented volume images, MHD format, # along with rendering configuration file. - name: liver-tumor-segmentation description: Segmentation of liver and tumor inferencing using DL trained model. container: image: clara/ai-livertumor tag: latest requests: gpu: 1 memory: 10240 input: - from: dicom-reader path: /input output: - path: /output name: segmentation - path: /publish name: rendering models: - name: segmentation_liver_v1 # name of the model registered with Clara Platform. Confirm by runniner clara list models. # dicom writer operator # Input1: `/input` containing a volume image file, in MHD format, name matching the DICOM series instance UID. # Input2: `/dicom` containing original DICOM instances, i.e. dcm file. # Output: `/output` containing the DICOM instances converted from the volume image, with updated attributes # based on original DICOM instances. - name: dicom-writer description: Converts MHD into DICOM instance with attributes based on the original instances. container: image: clara/dicom-seg-writer tag: latest variables: NVIDIA_SEG_LABELS: "[\"Liver\",\"Tumor\"]" input: - from: liver-tumor-segmentation name: segmentation path: /input - path: /dcm output: - path: /output name: dcm # register-volume-images-for-rendering operator # Input: Published original and segmented volume images, MHD format, along with rendering configuration file # from liver-tumor-segmentation operator. # Output: N/A. Input data will be sent to the destination, namely `renderserver` for Render Server DataSet Service. - name: register-volume-images-for-rendering description: Register volume images, MHD format, for rendering. container: image: clara/register-results tag: latest command: ["python", "register.py", "--agent", "renderserver"] input: - from: liver-tumor-segmentation name: rendering path: /input # register-dicom-output operator # Input: `/input` containing DICOM instances in the named output, `dicom` from dicom-writer operator. # Output: N/A. Input data will be sent to the destinations, namely DICOM devices, by the Clara DICOM SCU agent. - name: register-dicom-output description: Register converted DICOM instances with Results Service to be sent to external DICOM devices. container: image: clara/register-results tag: latest command: ["python", "register.py", "--agent", "ClaraSCU", "--data", "[\"MYPACS\"]"] input: - from: dicom-writer name: dcm path: /input
12.1.2. Executing the Pipeline¶
Please refer to the How to Run a Reference Pipeline using Model Repository section to learn how to register a pipeline, configure the DICOM Adapter, and execute the pipeline.
The model repository service uses Triton (TensorRT) Server version 20.02-py3 which does not currently support NVIDIA A100. Please use legacy pipeline service by
refering to How to Run a Reference Pipeline.