Teaching Neuroanatomy using the Allen Brain Atlas Resources

Teaching Neuroanatomy using the Allen Brain Atlas Resources Originally presented at: The Faculty for Undergraduate Neuroscience Annual Meeting July 2017 Terri Gilbert, Ph. D

Neuroanatomical concepts using the Allen Brain data Areal segregation What defines a brain area/region? Connectivity What areas are connected to each other? Development How does brain development progress?

Teaching Neuroanatomy ? Which resource? How to Interpret?

Best way to use this teaching module Which resource? ? Scientific Question What species? Familiarize yourself with the data in the desired resource How to Interpret? What developmental stage? Learn how to perform a search Technical Questions Understand the Allen Brain Atlas visualization Download the data

Example: ? Where is ddc located? Walk through the Adult Mouse data slides Which resource? Mouse Learn how to perform a gene search Technical Questions How to Interpret? Adult Learn to use the image viewers Download the data

Scientific Questions: 1. 2. 3. 4. 5. 6. 7. 8. Where is my gene of interest located? What genes are expressed in my region/area of interest? How does gene expression change over development? What structures are connected? Where does my region/area of interest project? What genes show a similar expression pattern to my gene of interest? How do I visualize the data? How does gene expression in mouse compare to human? …

Technical Questions: 1. 2. 3. 4. 5. How do I perform a search? How do I view/understand image data? How do I interpret heatmap data? How do I download the data? …

Glossary of Allen Institute Resources in this Module Allen Mouse Brain Atlas Genome-wide, anatomically comprehensive, cellular resolution in situ hybridization (ISH) images mapped into a 3 D reference space called the Common Coordinate Framework (CFF). Includes a suite of informatics tools including Differential Search, Correlative Search, Anatomic Gene Expression Atlas (AGEA) and synching to an anatomic reference atlas. Documentation | Online help Allen Developing Mouse Brain Atlas Colorimetric ISH gene expression of approximately 2000 genes across seven developmental stages mapped into a 3 D reference space. Includes expert manual gene expression annotation of embryonic stages and a suite of informatics tools including correlative search, AGEA and synching across stages to an anatomic reference atlas. Documentation | Online help | Manual Annotation Allen Mouse Brain Connectivity Atlas A high resolution atlas of long range neuronal projections in the adult mouse brain. Using an array of transgenic mice genetically engineered to target specific cell classes, targeting strategies to select distinct neuronal populations and serial twophoton tomography, this atlas uniquely describes structural connections. Informatics tools include registration into the CCF allowing for searching projection patterns and allows for a “virtual” retrograde search. Documentation | Online help | Tutorial

Glossary of Allen Institute Resources in this Module Allen Cell Types Database The initial step in characterizing the cellular components of the brain. The database is a multi-modal characterization of cells from the adult mouse visual cortex based on their electrophysiological, structural and gene expression characteristics. Single cell characterization includes accompanying models of cellular behavior. Future data releases will include data from human cortex. Documentation | Online help Allen Human Brain Atlas A unique multi-modal atlas mapping gene expression across the adult human brain. Integrating imaging data (MRI & DTI), histology, and gene expression derived from both microarray and ISH. Informatics processing provides anatomic and gene-based search coupled with a 2 D reference atlas. Documentation | Online help Brain. Span Atlas of the Developing Human Brain A broad and detailed anatomical analysis of gene expression across human brain development, comprising in situ hybridization, RNA-sequencing and microarray approaches, along with supporting neuroanatomical reference content. Documentation | Online help

JUNE References Novel in silico Method for Teaching Cytoarchitecture, Cellular Diversity, and Gene Expression in the Mammalian Brain JUNE (2007) Raddy L. Ramos, Phoebe T. Smith & Joshua C. Brumberg A Self-Study Tutorial using the Allen Brain Explorer and Brain Atlas to Teach Concepts of Mammalian Neuroanatomy and Brain Function JUNE (2009) Bruce G. Jenks Exercises in Anatomy, Connectivity, and Morphology using Neuromorpho. org and the Allen Brain Atlas JUNE (2015) Philip Chu, Joshua Peck, & Joshua C. Brumberg Other Resources Allen Institute for Brain Science Resources: http: //www. brain-map. org/overview/index. html Tutorials on the Resources: http: //www. brain-map. org/tutorials/index. html