Installation

Installation Options

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

To install TransBrain as a package in your environment, run:

pip install transbrain

To create a new Conda environment with TransBrain included, use environment.yml on Linux, or environment_win.yml / environment_mac.yml for Windows and macOS:

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 - 3.11). Key dependencies include:

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
tqdm==4.67.1
ipykernel==6.29.5
anndata==0.9.2

See the full list in the 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.

transbrain-main/
├── transbrain/
│   └── exampledata
├── test_transbrain.py (Unit Test file)
└── tests (Files used to verify installation)

python test_transbrain.py

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