
In the natural world, sensory experience unfolds as a continuous and dynamic process where past sensory input predicts the present. The brain utilizes this sequential flow of recent sensory information to make predictions, infer causal relationships between events, and to give rise to our perceptions. Traditionally, such higher cognitive functions were attributed to the computations undertaken in associative brain regions, while sensory areas (such as V1) were thought to serve as passive feature detectors. This longstanding view is now being challenged by compelling evidence showing the capacity of these areas for plasticity and complex computations such as forming spatial expectations, temporal associations, reward prediction, and categorial learning. Importantly, it has been established that sensory processing is not solely determined by the system's current sensory inputs but also strongly influenced by preceding sensory inputs, a phenomenon known as hysteresis.This phenomenon has been characterized in detail in the visual system, with prominent examples that include adaptation, repetition suppression, prediction suppression and facilitatory history effects. However, previous work predominantly focused on the neuronal dynamics over short time scales, ranging from milliseconds to several minutes, in response to a limited set of synthetic stimuli. Moreover, much of our current knowledge relies on recordings from the primary visual cortex and on interpretations that emphasize modulation of single cells’ activity rather than analysis of population-level dynamics. Consequently, the extent to which prior experience over longer timescales shapes neuronal representations, and specifically representations of more ethologically relevant natural stimuli, remains unclear. It also remains unclear whether and to what extent the effects of prior experience on such neuronal representations differ along the visual system's hierarchical structure.
This platform builds on turn-key lightsheet microscopes to image mouse brains at high resolution and throughput. Analysis of the resulting volumetric images, including registration to standard brain coordinates and segmentation and counting of individual neurons, is fully automated.
This platform uses a 2-photon microscope SLAP2 that records patterns of synaptic input and output in individual neurons at hundreds to thousands of frames per second in mice performing complex behaviors, using a flexible scan system that combines a digital micromirror device (DMD) with a high-speed scanner.
The Scientific Instrumentation and Process Engineering (SIPE) team is a shared engineering resource within the Allen Institute, focused on enabling and scaling cutting-edge bioscience through integrated hardware and software systems.
The Population Calcium Imaging platform measures changes in neural dynamics over long time scales as animals learn and behave.
This team performs a variety of surgical procedures, including stereotaxic injections and implanting chronic cranial windows and Neuropixels probes.
This platform implements pioneering technology for highly reproducible, targeted, brain-wide, cell-type-specific electrophysiology to record neural activity from defined neuron types across the brain. Analysis and quality control of the electrophysiology data are fully automated.
This platform combines innovative histology, ExA-SPIM microscopy, image handling, and machine learning to map the morphology and molecular identity of individual neurons across the whole brain at high throughput.
This platform enables optical measurement of neural activity and neurotransmitter release in populations of neurons to study neural circuit dynamics in behaving animals.
The Behavior platform uses advanced technology to implement a standardized, modular, multi-task virtual reality gymnasium for mice, with the goal to study brain function across different behaviors at scale.







