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Setup & Usage

  • Installation
    • Installation Options
    • Python Dependencies
    • Unit Test
  • User Guide
    • Online Mapping
    • General Use
    • Advanced Use
  • Supported Atlases
    • Human Brain Atlases
    • Mouse Brain Atlas

Tutorials

  • Method Glossary
    • Datasets
    • Methods or Concepts
  • Online Mapping
  • Basic use 1: Mouse to human
    • Step 1: Prepare input data
      • Visualizing mouse phenotype data
    • Step 2: Initialization
    • Step 3: Mapping
  • Basic use 2: Human to mouse
    • Step 1: Prepare input data
      • Visualizing human phenotype data
    • Step 2: Initialization
    • Step 3: Mapping
  • Case 1: Analyzing the conservation of resting-fMRI gradients
    • Introduction
    • Mapping mouse gradient to human
    • Compare with human Gradient
    • Cross-species correlation
  • Case 2: Annotating optogenetic circuits
    • Introduction
      • Data
    • Translating mouse stimulated pattern to human
    • Annotating using NeuroSynth.
  • Case 3: Linking gene mutations to imaging phenotype deviations
    • Introduction
      • Data
    • Translating mouse mutation patterns to human
    • Calculate individual gene risk score
  • Advanced Use
    • Transcriptional Data Integration
      • Introduction
        • AHBA data
        • Human single-nucleus data
        • Mouse spatial transcriptomic data
      • Selection of cortical stable genes
      • Selection of subcortical stable genes
      • Selection of all stable genes
      • Thresholds of cortex
      • Thresholds of subcortex
      • Thresholds of all
    • DNN Model Training
      • Introduction
        • Model architecture
        • Region-specific embeddings
    • Graph-based Random Walk
      • Introduction
        • Human diffusion-based tractography
        • Mouse Tracer
        • Embedding space generated from Human-Mouse graph
      • Define human and mouse ROIs
      • Load anatomical hierachy constraint information
    • Bidirectional Mapping

API

  • API Reference
    • Fetching Atlases
      • fetch_human_atlas()
      • fetch_mouse_atlas()
    • Base Functions
      • get_region_phenotypes()
    • Mapping Functions
      • SpeciesTrans
        • SpeciesTrans.atlas_type
        • SpeciesTrans.regions
        • SpeciesTrans.embeddings
        • SpeciesTrans._load_embeddings()
        • SpeciesTrans._dual_mapping()
        • SpeciesTrans._translate()
        • SpeciesTrans.mouse_to_human()
        • SpeciesTrans.human_to_mouse()
    • Visualization Functions
      • map_phenotype_to_nifti()
      • plot_mouse_phenotype()
      • plot_human_phenotype()
      • plot_surface_phenotype()
  • Development Functions
    • Transcriptional Data Process
      • Preprocess_Sn
        • Preprocess_Sn.dataset_qc()
        • Preprocess_Sn.dataset_normalized()
        • Preprocess_Sn.dataset_common_genes()
        • Preprocess_Sn.dataset_batch_correct()
        • Preprocess_Sn.dataset_smooth()
        • Preprocess_Sn.dataset_scaled()
        • Preprocess_Sn.preprocess_pipeline()
    • Data Integration
      • stable_gene_filter()
      • calculate_thresholds()
      • DataIntegrator
        • DataIntegrator.__init__()
        • DataIntegrator.run()
        • DataIntegrator.pool_construction()
        • DataIntegrator.clean_pool()
        • DataIntegrator.weighted_average()
        • DataIntegrator.downsample_data()
        • DataIntegrator.generate_integrated_anndata()
    • DNN
      • calculate_rank()
      • transform_human_mouse()
      • independent_test()
      • DnnPipeline
        • DnnPipeline.cfg
        • DnnPipeline.logger
        • DnnPipeline.execute()
        • DnnPipeline.train()
        • DnnPipeline.trans()
        • DnnPipeline.test()
        • DnnPipeline._process_single_dataset()
        • DnnPipeline._train_single_model()
    • Graph Walk
      • generate_embeddings()

Other

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