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Conversion of Adesnik lab calcium imaging data to the NWB:N format

Key Investigators

Evan Lyall (Evan Lyall, UC Berkeley)

Project Description

The goal of this project is to convert the whole-cell electrophysiology data from the Sabatini lab to the NWB format. This data includes voltage-clamp and current-clamp recordings from neurons in acute brain slices. This data is typically analyzed for the presence or absence of synaptic responses or changes in membrane potential. However, we often extract other features such as response amplitude, latency, onset and offset kinetics, frequency of synaptic events or action potentials, and variability of responses in repeated trials. Therefore, a standard toolset to analyze this data in the NWB data format would also be useful. Finally, we often record electrophysiology data in tandem with 2-photon imaging, and would like to be able to incorporate imaging data into the NWB:N file format.

Objectives

  1. Objective A. Develop understanding of NWB:N format for multi-plane calcium imaging data
  2. Objective B. Save one Adesnik lab calcium imaging experiment into the NWB:N file format
  3. Objective C. Build out basic analysis notebook
  4. Objective D. Cleanup conversion script to convert all Adesnik lab data to NWB:N format

Approach and Plan

  1. Prior to the hackathon: read through NWB:N documentation and prepare conda environment
  2. Convert a single movie to NWB:N format including all experiment metadata
  3. Write analysis notebook that loads in NWB:N data and interactively plots different views of the data
  4. Polish conversion script to generalize to all Scanbox data in the lab

Progress and Next Steps

Materials

Background and References