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PUMA Challenge Evaluation Track 1

This repository contains a Dockerized environment for running the PUMA Challenge Evaluation track using CUDA 12.1. The container includes all necessary dependencies to execute the model and run inference on input data.

Prerequisites

  • Docker (Ensure that Docker is installed and supports GPU with CUDA 12.1 or newer)
  • NVIDIA Docker Toolkit for GPU support

Build the container

You can build the Docker image using the build.sh script. Ensure GPU support is enabled.

Running the container.

Use the test_run.sh script to run the container.

Input & Output

Input will be mounted at /input and consists of 2 files:

  • melanoma-3-class-nuclei-segmentation.json contains the nuclei predictions in "Multiple Polygons" format.
  • images/melanoma-tissue-mask-segmentation/<uuid>.tif contains the tissue predictions, where pixels should be given the following values: 'Background': 0, 'Stroma': 1, 'Blood Vessel': 2, 'Tumor': 3, 'Epidermis': 4, and 'Necrosis': 5

In the /test directory, two example input cases can be found.

Output will be generated at /output/metrics.json for both nuclei and tissue metrics.

Saving the container

Use save.sh to save the container.

Ground Truth

Note that all ground truth data has been removed from this repository.