Each of our research programs is oriented toward creating and sharing resources that will drive scientific progress by the global neuroscience community. Our commitment to open science has led us to projects that will help establish the standards needed by the scientific community to better understand how the brain processes information, and provide the framework needed to answer future questions about the brain.

Cell Types

There are 86 billion neurons in the human brain, and no two are exactly alike. In order to understand how the brain works, we need to understand each of its parts and how those parts interact with one another. The ultimate goal of the Cell Types program is to establish the equivalent of a “periodic table” for the brain: a comprehensive list of parts that captures how different cells are shaped, the genes they express, their function within circuits; and to understand the hierarchical organization of cell types by building a taxonomy utilizing the key features (genes, shapes, physiological properties, etc.) for classifying neuronal diversity.

The Cell Types program is exploring this question in the visual cortex and lateral geniculate nucleus (LGN) of the mouse brain and human temporal lobe by examining individual neurons by multiple modalities, including electrophysiology and accompanying models, transcriptomics, morphology and connectivity. Creating a robust wiring diagram of the brain will require experimental approaches that illuminate the molecular complexity of synapses, including electron microscopy and array tomography, as well as methods to discover the functional wiring of cells, which can be elucidated using techniques such as multi-patch electrophysiology.

One output of this program is the Allen Cell Types Database: the first resource of its kind to present these multiple types of data from single cells, with the goal of enabling the community to investigate the different types of cells in the brain. A wiring diagram of neocortical regions of the brain will be further developed as part of our connectivity work, which will add more data from new Cre line transgenic mice.


Being able to see what is happening in the brain as it happens is crucial to understanding a highly dynamic process like vision. Multiple areas of the brain process visual information in parallel, and in order to advance from an instantaneous response to visual cues to recognizing and interpreting those visual cues, a complex interplay of signals must be exchanged rapidly between different regions of the cortex. Researchers in the BrainTV program are exploring how the brain processes distinct features of the visual world by recording the activity of different cortical areas and their composite cells in individual animals as they perform visual tasks. 

A rich combination of genetic tools, functional imaging techniques, behavior training and data analysis technology--including our newest resource, the Allen Brain Observatory--will allow for the systematic collection of data that will ultimately provide a window into the process of vision in the mouse brain at the level of single cells or populations and in real time. The compendium of these data will be provided to the neuroscience community, and resulting knowledge will be integrated into detailed simulations of the brain.


The Allen Institute for Brain Science has built a legacy on our product releases, and we are motivated to adopt a data, tools and knowledge-based framework toward product development to structure our output and to best serve the needs of our users. We emphasize large-scale multimodal data generation, feature extraction and data browsing and mining tools, and synthesis of knowledge and descriptive summary vignettes.