Exploring neural data from the Allen Institute for Neural Dynamics

The Allen Institute for Neural Dynamics (AIND) began in 2021 with the mission to decode the brain's complex circuitry and understand how its activity gives rise to complex behaviors, decision-making, and memory. To do this we are establishing platforms that generate complex brain wide data aimed at including neurophysiology, behavior, and molecular anatomy. In this workshop, we will introduce our open data platform and spotlight two of these platforms, the data they produce and what types of things we are doing with them.

We will first introduce anatomy data collected using our expansion assisted selective plane illumination microscope (exaSPIM). These high-resolution whole brain images allow us to reconstruct the complete morphology of individual neurons in the intact brain. We will work with these reconstructions during our workshop, examining the dendritic and axonal structures of individual neurons and explore quantitative methods to classify neurons based on morphology – structural features, projection targets and projection strengths. 

Second, we will explore electrophysiological data collected with Neuropixels probes. We will focus on data that is being collected as part of a “Cell Type Look-up Table”. These data have been collected from the mouse striatum, aimed to create a ground-truth dataset to differentiate striatal cell types based on their extracellular electrophysiological properties. Using optotagging protocols, specific transgenically defined cell-types can be isolated using optogenetic stimulation, with the goal of being able to predict the neuron’s transgenic identity based on their firing properties. 

For each data modality, we will lead a hands-on demo to introduce participants to the data, what it is, how to access and use it. Participants will then have time to work with the data, exploring their own questions in these data. Some python coding experience is expected (e.g. numpy, matplotlib, pandas)

Learn more about the Allen Institute:
https://alleninstitute.org