.. _build_method: Advanced Use ======================================== - Here we provide a step-by-step guide to follow the TransBrain construction pipeline. - If you have more specific needs (such as constructing mapping matrices based on your own data or atlases), this tutorial will help you. - On each page you can find a brief introduction of the data and methods, for detailed description please refer to our `preprint `_. - Due to the large data size, the dataset is not included in the GitHub repository. If needed, you can download it from the link in ``pipeline/datasets/README.md`` and place it in the same directory. 1. **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. 2. **Graph-based Random Walk** - A heterogeneous graph was constructed to connect brain regions within and across species. - Latent embeddings capturing integrated transcriptomic, anatomical, and connectivity information were generated. 3. **Bidirectional Mapping** - `Dual-regression <./methods/mapping.rst>`_ method was employed to map phenotypes cross species, using the latent embeddings defined previously. .. toctree:: :maxdepth: 1 :caption: Steps pipeline/run_pipeline/integration.ipynb pipeline/run_pipeline/dnn.ipynb pipeline/run_pipeline/graph_embedding.ipynb ./methods/mapping