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 from 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
Ultrastructural Connectomics
The Machine Intelligence from Cortical Networks (MICrONS) program seeks to reverse-engineer algorithms of brain function. Output from one of the projects is accessible through MICrONS Explorer, a portal to explore the wiring of the mouse brain and all its components at sub-cellular resolution. The data include electron microscopy-based reconstructions of cortical circuitry from mouse visual cortex, with corresponding functional imaging. This was created by a consortium of laboratories from the Allen Institute, Princeton University, and Baylor College of Medicine, and with support from the IARPA MICrONS program.
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.
Mesoscale Connectivity in Aging and Alzheimer’s Disease
Axonal projections were labeled with stereotaxic injections of viral tracers in mouse models of Alzheimer’s disease and their aged littermates. Whole brain axonal trajectories were quantified using the standardized platform for the Allen Mouse Brain Connectivity Atlas to generate a database of neural projections in aging and diseased mice. Amyloid beta plaques were also labeled in mice with amyloid pathology, and brain-wide plaque density was quantified using an automated pipeline. This dataset can be compared with the projections of young adult (p56) mice in the Allen Mouse Brain Connectivity Atlas to identify differences in anatomy and connectivity that occur in aging and Alzheimer’s disease.
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