Welcome to 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.
Key Features
🧬 Spatial Transcriptomic Matching
We integrated complementary human transcriptomic datasets, including microarray data and large-scale single-nucleus RNA sequencing data.
A detached deep neural network model was trained on the integrated transcriptomic data to learn region-specific latent embeddings that are generalizable across species.
🧠 Graph-based Random Walk
A heterogeneous graph was constructed to connect brain regions within and across species.
Intra-species edges were defined based on anatomical connectivity, using viral tracer data for mouse and diffusion-based tractography for human from Human Connectome Project (HCP).
Cross-species edges were determined by transcriptomic embeddings learned from the first phase, constrained by coarse-scale anatomical hierarchies.
Establishing a unified cross-species latent space incorporating anatomical hierarchies and structural connectivity.
🔄 Bidirectional Mapping
Dual-regression method was employed to map phenotypes cross species, using the latent embeddings defined previously.
Method Glossary
The process of building TransBrain involves several steps, which may be confusing for those who are not from related fields. To help users better understand the methodology, we set up a Method Glossary page.
What can TransBrain do?
TransBrain offers many promising applications. You can learn how to implement these functions in the Tutorials section of this documentation or through our GitHub repository.
Inferring the conservation of whole-brain phenotypes.
Transforming and annotating whole-brain functional circuits.
Linking specific mouse models with human diseases.
Usage Options
To accommodate the different needs of users, we provide three levels of usage options. See details in User Guide.
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, you can refer to our API Reference and Tutorials for detailed guidance.
Advanced Use
If you want to understand the detailed methodology of TransBrain or adapt it to your specific needs, please refer to Advanced Use section.
Contents
Setup & Usage
Tutorials
API
About
📜 [Our Preprint]
📧 For questions, contact the author: Shangzheng Huang (huangshangzheng@ibp.ac.cn) and cc TransBrain (transbrainmapping@gmail.com).