TransBrain

TransBrain is an integrated computational framework for bidirectional translation of brain-wide phenotypes between humans and mice. Specifically, TransBrain provides a systematic approach for cross-species quantitative comparison and mechanistic investigation of both normal and pathological brain functions.

What can TransBrain do?

1. Inferring the conservation of whole-brain phenotypes.

2. Transforming and annotating whole-brain functional circuits.

3. Linking specific mouse models with human diseases.

Further Reading

If you wish to learn more about the construction details of this method, please refer to our article: https://www.biorxiv.org/content/10.1101/2025.01.27.635016v1 (in preprint).

Installation

TransBrain is on pypi: https://pypi.org/project/transbrain/

To install TransBrain as a package, run:

pip install transbrain

You can also create a conda environment from the environment.yml file:

• First, clone this repository,

git clone https://github.com/ibpshangzheng/transbrain.git

• Then, create the environment,

cd transbrain
conda env create -f environment.yml

• Activate the environment,

conda activate transbrain_env

Python Dependencies

The project mainly depends on Python (>= 3.8.5).

matplotlib==3.7.5,
matplotlib-inline==0.1.7,
nibabel==5.2.1,
nilearn==0.10.4,
numpy==1.24.4,
openpyxl==3.1.5,
pandas==2.0.3,
scikit-learn==1.3.2,
scipy==1.10.1,
seaborn==0.13.2,
six==1.17.0

See full list in environment.yml file.

Unit Test

• We provide a Python Unit Test module to check whether the installation was successful.
• Clone our repository and run this file. Make sure you are in the ​root directory​ (where test_transbrain.py is located) before running the test.

File Structure

transbrain-main/
├── transbrain/
│ └── exampledata/
├── test_transbrain.py # Unit Test file
└── tests/ # Verification files

python test_transbrain.py

• If you see the message 🎉 TransBrain installed successfully!!!, it means that TransBrain is ready to use.

Usage Options

To accommodate the different needs of users, we provide three levels of usage options. You can see detailed documentation of TransBrain here

Online Mapping

• The easiest way to get started with TransBrain. We provide a code-free website (https://transbrain.streamlit.app/), enabling users to directly upload your data for online mapping and visualization.

General Use

• If you want to use TransBrain to map your data and have some basic knowledge of Python, we provide Tutorial Cases demonstrating how to apply TransBrain for cross-species translation and comparison, which includes:

  • Basic example of mapping mouse phenotypes to human.

  • Basic example of mapping human phenotypes to mouse.

  • Case 1: Analyzing the conservation of resting-fMRI gradients.

  • Case 2: Annotating the optogenetic circuits in mice using Neurosynth.

  • Case 3: Linking gene mutations to imaging phenotype deviations in autism.

Advanced Use

• If you want to understand the detailed methodology of TransBrain or adapt it to your specific needs, the construction pipeline of TransBrain is also publicly available in this GitHub repository.

More detailed tutorials and API references of TransBrain can be found in our documentation. This helps seamless integration into your existing workflows. 🚀

License

This project is covered under the Apache 2.0 License.

Support

For questions and comments, please file a Github issue and/or email Shangzheng Huang(huangshangzheng@ibp.ac.cn) and cc TransBrain (transbrainmapping@gmail.com).