Exploring Cortex in a High-Throughput Manner

Sunday, 16 February 2014
Crystal Ballroom A (Hyatt Regency Chicago)
Christof Koch , Allen Institute for Brain Science , Seattle, WA

In early 2012, the Allen Institute for Brain Science announced a 10-year high-throughput plan to understand the structure and function of neocortex and associated satellite structures by mapping the transcriptional, morphological, and physiological characteristics of cell types within the mouse and human cortico-thalamic complex, how these cells connect to form a network, and how they encode, relay, and process information via appropriate computer simulations. Work in the mouse is focused on the thalamo-cortical system underlying vision and visual perception in behaving animals. Work in the human will use cortical tissue from four distinct sources: post-mortem whole brain, surgical resected medial temporal lobe, fetal tissue and inducible-pluripotent stem cells differentiated into forebrain neurons. We are building pipelines to analyze the cellular morphology, electrophysiology, electrical behavior in terms of models and transcriptome of 1,000s of mice and human neurons and to map the structural and functional connectomes at both micro- and meso-scopic scales. The resulting neuroscientific observatories will generate massive, multimodal, open-access datasets through standardized, reproducible and scalable methods.

Launched in late 2004, the Allen Brain Atlas at http://www.brain-map.org/ is a set of large-scale resources (> 1 million images, 400 TB), integrating genome-wide gene expression, structural connectivity, and neuroanatomical data across the entire brain for developing and adult humans, non-human primates and laboratory mice, complemented by high-resolution, cellular-based anatomical connectivity data in >1,000 mice. The Atlas is the single largest integrated database of neuroscience data worldwide, with ca. 50,000 monthly unique users from academia and the pharmaceutical industry. Linking developmental transcriptomics with detailed structural neuroanatomy, the Atlas is a foundational resource for understanding human brain disease, providing a spatiotemporal map for genes associated with disease, as well as for studies of brain function in model organisms by linking anatomical structure and cell type to their causative gene expression programs. All data is freely available without any restrictions.