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Connectivity Matrices

To understand the brain, we need to understand not only its building blocks, the cells, but how those building blocks fit together and interact with one another. The mammalian “connectome” is complex;  the brain can be measured at different scales, and with diverse experimental modalities. Here, data and information is available about projects that contribute to our knowledge about the structure of the brain and its connections.

Mesoscale Connectivity

The Allen Mouse Brain Connectivity Atlas is a three-dimensional, high-resolution mesoscale map of neural connections in the mouse brain. Axonal trajectories from a broad range of brain regions were mapped using a standardized platform to generate a comprehensive database of neural projections. Through a panel of over 100 transgenic mice genetically engineered to target cell classes, the Allen Mouse Brain Connectivity Atlas provides brain-wide coverage - and select data fron retina. This neural connectivity information complements the Allen Institute’s gene expression atlases and Brain Observatory, and thus provides opportunities to help understand how genes contribute to connectivity formation and function. 

Access data portal  | Access the Allen Brain Explorer - 3D  |  Publication

Synaptic Physiology

The scale and complexity of neural circuits pose experimental challenges, leading to an incomplete understanding of how different cell types are connected and the signaling that takes place at those connections. The Synaptic Physiology project contributes to our understanding of cortical circuits by investigating synaptic signaling via in vitro patch clamp physiology. The dataset provides insight into the connection probability, synaptic strength, and short-term plasticity in mouse primary visual cortex and human middle temporal gyrus. Analysis tools and software applications are available to facilitate exploration of this dataset.

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Ultrastructural Connectomics

Researchers from the Allen Institute for Brain Science are working in collaboration with Baylor College of Medicine, Princeton University and Harvard Medical School on the IARPA MICrONS project. The goal is to create the largest ever roadmap of connections in the mammalian brain. Our electron microscopy team is contributing to this enormous effort by imaging billions of tiny synaptic connections in a cubic millimeter of mouse neocortex.  Learn more about this project here.