external_model_installation.md

External Model Installation Guide

This guide covers the installation of optional external segmentation models for SPROUT.

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Table of Contents

• SAM (Segment Anything Model)
• nnInteractive

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SAM (Segment Anything Model)

SPROUT supports integration with Segment Anything Model for enhanced segmentation capabilities.

If you want to use prompts generated from SPROUT in SAM, you can install SAM models like SAM and SAM2. Currently only supports SAM1 and SAM2-based models

Core Dependencies

pip install torch torchvision torchaudio
pip install opencv-python-headless

⚠️ For optimal performance, we recommend using GPU-enabled PyTorch. You can find the correct installation command based on your system here:
https://pytorch.org/get-started/locally/

📦 Install Segment Anything Models

You also need to install the SAM and/or SAM2 libraries:

• SAM (Segment Anything Model)

  git clone https://github.com/facebookresearch/segment-anything.git
  cd segment-anything
  pip install -e .

• SAM2 (Segment Anything v2)

  git clone https://github.com/facebookresearch/sam2.git
  cd sam2
  pip install -e .

nnInteractive

See Official repo for detail information

You need a Linux or Windows computer with a Nvidia GPU. 10GB of VRAM is recommended. Small objects should work with <6GB.

Install PyTorch

Go to the PyTorch homepage and pick the right configuration. Note that since recently PyTorch needs to be installed via pip. This is fine to do within your conda environment.

For Ubuntu with a Nvidia GPU, pick 'stable', 'Linux', 'Pip', 'Python', 'CUDA12.6' (if all drivers are up to date, otherwise use and older version):

pip3 install torch torchvision --index-url https://download.pytorch.org/whl/cu126

Install nnInteractive

Either install via pip: pip install nninteractive

Or clone and install this repository:

git clone https://github.com/MIC-DKFZ/nnInteractive
cd nnInteractive
pip install -e .