BraDiPho: Brain Dissection Photogrammetry

BraDiPho is an innovative framework for exploring human brain anatomy by integrating ex-vivo microdissection and in-vivo tractography data. It leverages photogrammetry to provide detailed 3D models of brain dissections, enabling interactive and educational insights into white matter structures.

Data Source and Documentation

BraDiPho provides tools, models, and tutorials for integration and exploration of brain anatomy data. Learn more on the official website:

• BraDiPho Website
• BraDiPho OHBM Talk 2023
• BraDiPhoPy Repository
• Registration Files on Zenodo

Features

• Integration of Ex-Vivo and In-Vivo Data: Combines microdissection and tractography in a common neuroradiological space.
• High-Resolution 3D Models: Includes photogrammetric reconstructions for detailed exploration.

Running BraDiPho with Docker or Singularity

The most efficient way to use this pipeline is through Docker or Singularity, ensuring all dependencies are managed and isolated.

Building the Docker or Singularity Image

To build the required container, use the following commands:

Docker:

docker build . -t "bradipho" --rm --no-cache

Singularity:

singularity build bradipho.sif docker-daemon://bradipho:latest

Example Command to Launch the Pipeline

Singularity Execution:

singularity exec bradipho.sif bash /bdp_registration_utils/launch_registration.sh ${PATH_TO_INPUT_DATA}/ sub-01 ${PATH_TO_OUTPUT_DATA}

• Replace ${PATH_TO_INPUT_DATA} with the path to your input data directory.
• sub-01 is an example subject identifier; adjust as needed. (sub-01, sub-02, sub-04, sub-10, sub-16, sub-17, sub-18, sub-19)

This setup allows you to easily process your data and integrate it into the BraDiPho framework.