Malaria Microscopy Classification Pipeline

0.7.4

The Malaria Microscopy Classification pipeline is one of the reference pipelines provided with Clara Deploy SDK. A pre-trained model for classification of malaria from PNG images representing the microscopy slides is used in the pipeline. This pipeline depends on the Clara Deploy CLI to send PNG images and trigger a job.

Once the pipeline is started, the AI model classifies input images and saves the output as new images with the classification label burnt-in on top of the images. If the class category of a specific image is “parasitized”, the operator burns in the letter “T” to the upper left corner of the output image, otherwise the letter “F” is written out. The output images can be downloaded by Clara CLI and viewed by any PNG image viewer such as GIMP.

The Malaria Microscopy Classification pipeline is defined in the Clara Deploy pipeline definition language. This pipeline utilizes built-in reference containers to construct the following operator:

  • The ai-app-malaria operator performs AI inference against the NVIDIA TensorRT Inference server to generate malaria classification images.

The following is the details of pipeline definition, with comments describing each operator’s functions as well as input and output.

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api-version: 0.3.0 name: malaria-pipeline operators: - name: ai-app-malaria description: Classifying Malaria Images container: image: clara/ai-malaria tag: latest input: - path: /input output: - path: /output services: - name: trtis container: image: nvcr.io/nvidia/tensorrtserver tag: 19.08-py3 command: ["trtserver", "--model-store=$(NVIDIA_CLARA_SERVICE_DATA_PATH)/models"] requests: gpu: 1 connections: http: - name: NVIDIA_CLARA_TRTISURI port: 8000

Please refer to the section <a href="/RunningReferencePipeline.html#run-reference-pipelines-using-local-input-files" target="_self">Run Reference Pipelines using Local Input Files</a> on How to run a Reference Pipeline.

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