AAuRA Benchmark Preprocessing

Authors: Katy Scott, Kaitlyn Kobayashi

Contact: bhklab.katyscott@gmail.com

Description: Preprocessing of datasets for use in the AAuRA Benchmarking tool.

Note: August 2026, from Katy

This code is being replaced by the nifti indexer capability in Med-ImageTools and the ab-testing. Useful information that can be extracted from this:

• utils_models.py --> metadata requirements for the dataset index to be fed into Kaitlyn's AAuRA pipelines (nnInteractive, MedSAM2, etc.)

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Set Up

Prerequisites

Pixi is required to run this project. If you haven't installed it yet, follow these instructions

Installation

1. Clone this repository to your local machine
2. Navigate to the project directory
3. Set up the environment using Pixi:

pixi install

Documentation

Click here to view the full documentation.