Towards a Complete Description of the Circuitry Underlying Sharp Wave-Mediated Memory Replay

Back to U19 Main Page

 

U19 Project:  Modelers:  Aaron Milstein, Ivan Raikov, and Prannath Moolchand; PI:  Ivan Soltesz; Stanford; modeling hippocampal circuits. The level of biophysical detail of our models is high. We use the simulation environment NEURON. We write mostly code in python. We run our models using collective operations enabled by MPI parallelism. We are comparing alternative theories to explain sparse population codes of space during exploration, and offline memory sequence replay during sleep. Our models point to important roles for synaptic plasticity, nonlinear input summation in dendrites, and specific classes of inhibitory cells.

Soltesz U19 Hippocampal Modeling Project Summary  

soltesz_u19_hippocampal_modeling_project_summary.pptx

soltesz_u19_hippocampal_modeling_project_summary.pdf

  • Description of how Data Science Core is complying to the criteria of the FAIR principles:

We have publicly shared data in the DANDI archive formatted in NWB format. The NWB format ensure that the data has the necessary metadata to be reusable, and posting it publicly makes the data Accessible. We are using this dataset to help the DANDI team develop their platform around user needs, ensuring Interoperability, and to scrape the appropriate data to enable structured search so that the data is Findable.

  • List of Data Types in U19:
    • Optical physiology
      • Calcium imaging
      • Regions on interest and DF/F traces
      • Photometry
    • Behavior
      • 3D point cloud behavioral data
      • Position tracking
      • trials and decisions
    • Extracellular electrophysiology
      • Voltage traces
      • Local field potential
      • Spike times
  • Common Data Elements in U19: All groups hare tracking neuron-level activity in the hippocampus. Many of the associated analysis can be used across labs.
  • Data Sharing goals in U19:
    • Facilitate sharing within Ripple U19 using NWB
    • Publicly share datasets with the community in NWB
  • Data science tools being used in project:
  • Data science tools being developed for project:
  • Data science approaches to be shared with other U19’s:
  • Data science challenges that could benefit from discussion with other U19’s:
    • ​​​​​​​How to lower the barrier of data standardization
    • How to integrate with tools that others are building
    • Provenance tracking

 

Data Reuse Abstract

Our U19 group studies the cellular bases of memory consolidation, particularly how sharp wave ripples serve as a transfer mechanism between hippocampus and neocortex. We use cutting-edge large-scale electrophysiology and optophysiological recording technologies to study and manipulate identified cell types in behaving animals, coupled with data-driven simulations.  Our goal is to elucidate the cellular mechanisms responsible for memory replay and its role in memory transfer and consolidation. The methods used by our group can be applied to many situations in which brain mechanisms of behavior and cognition are explored.

Our data spans several neurophysiological techniques that provide insights into the mechanisms sharp wave ripples:
- Large-scale electrophysiological recordings of freely moving mice and rats in various learning and navigational tasks. 
- Behavioral measures span from classic position-and-heading-direction measures to a high-resolution continuous monitoring of the entire movement repertoire of the animal
- Calcium imaging data and extraction of sharp wave ripples from the optical signal.
- Novel fiber photometry and voltage imaging techniques that provide unprecedented information about cell types-specific contributions to population cooperativity.

We are particularly interested in application of analytical tools that could help determine specific cellular connectivity and contributions to the sharp wave ripple processes, and can assist our large-scale computational model building. Related analytical topics could include:
- Tuning properties of hippocampal cells in various tasks
- Examination and reliability of sharp wave ripples extracted from calcium imaging data
- Novel analysis or visualization techniques applied to the simulated neural activity output by our large-scale computational model

Link to Data/Model Reuse abstract, [Link] 

 

 

2021 Brain PI Meeting

Update:

Link to Poster:

Demo:

 

Back to U19 Main Page

Table sorting checkbox
Off