Module 04: Neuroanatomy and Circuit Architecture

Learn how the brain is organized into regions, layers, and systems—and how those structures shape connectivity.

🧭 Mapping the Brain: Gross and Fine Anatomy

The brain is organized into regions (e.g., cortex, hippocampus, thalamus) that carry out specialized functions. Each region has distinct anatomy visible at both macroscopic and microscopic levels. Understanding where a dataset comes from is key to interpreting its significance.

  • Gross anatomy: lobes, gyri, sulci, ventricles
  • Microscopic anatomy: cortical layers, hippocampal subfields
  • Common brain atlases and reference frameworks

🏗️ Layers, Columns, and Microcircuits

Within brain regions, neurons are arranged in stereotyped patterns. In the cortex, this includes six layers and repeating columnar structures. These features shape how circuits function and must be considered during analysis.

  • Columnar organization of the neocortex
  • Laminar inputs and outputs
  • Thalamocortical and corticocortical circuits

🔬 Neuroanatomy in EM Datasets

Connectomics volumes may span multiple layers or regions. Accurate annotation requires contextual awareness. Tools like Neuroglancer and 3D viewers can assist in orienting within a dataset.

  • Identifying regions and layers in EM volumes
  • Comparing volumes: MICrONS vs. H01 vs. FlyWire
  • Embedding anatomical knowledge into AI workflows

🎯 COMPASS Integration

  • Knowledge: Structures of the brain and regional functions
  • Skills: Spatial reasoning, image interpretation, reference use
  • Character: Precision, curiosity, discipline
  • Meta-Learning: Mapping new knowledge to spatial structures

📚 References & Resources

✅ Assessment

  • Label the six layers of cortex and describe a function of each
  • Use an EM viewer to identify region-specific features
  • Summarize how brain region impacts connectome structure