Skip to content
@LorenFrankLab

Loren Frank Lab at UCSF

The Frank Lab

https://franklab.ucsf.edu/

Our laboratory focuses on the circuitry of the hippocampus and anatomically related regions. We use a combination of techniques, including large scale multielectrode recording, real-time signal processing and targeted optogenetic interventions and behavioral manipulations of awake, behaving animals to understand how the brain learns, remembers and decides.

lab picture

Main Data Processing Pipelines

  • spyglass - Neuroscience data analysis framework using NWB files and Datajoint pipelines
  • trodes_to_nwb - Convert trodes .rec files to the NWB 2.0+ data format
  • NWB Yaml creator - Create standardized metadata YAML files for use with trodes_to_nwb

Useful Data Processing Packages

Code for Papers

  • Joshi, A., Denovellis, E.L., Mankili, A., Meneksedag, Y., Davidson, T.J., Gillespie, A.K., Guidera, J.A., Roumis, D., and Frank, L.M. (2023). Dynamic synchronization between hippocampal representations and stepping. Nature. 2023 Apr 12;10.1038/s41586-023-05928-6. [Paper] [Code] [Data]
  • Denovellis EL, Gillespie AK, Coulter ME, Sosa M, Chung JE, Eden UT, et al. Hippocampal replay of experience at real-world speeds. eLife. 2021 Sep 27;10:e64505. [Paper] [Code] [Data]
  • Gillespie AK, Astudillo Maya DA, Denovellis EL, Liu DF, Kastner DB, Coulter ME, et al. Hippocampal replay reflects specific past experiences rather than a plan for subsequent choice. Neuron. 2021 Aug;S0896627321005730. [Paper] [Code] [Data]

Pinned Loading

  1. spyglass spyglass Public

    Neuroscience data analysis framework for reproducible research built by Loren Frank Lab at UCSF

    Jupyter Notebook 94 43

  2. rec_to_binaries rec_to_binaries Public

    A python package that converts SpikeGadgets rec files in the Frank lab directory format to more useable binaries with the same directory format.

    Jupyter Notebook 2 6

  3. rec_to_nwb_yaml_creator rec_to_nwb_yaml_creator Public

    Create YAML files for rec-to-NWB Conversion

    JavaScript 1

  4. track_linearization track_linearization Public

    Linearize 2D position to 1D using an HMM

    Python 6 3

  5. Gillespie_Neuron_2021 Gillespie_Neuron_2021 Public

    analysis code for Gillespie et al, Neuron 2021

    MATLAB 1

  6. Joshi_et_al_2023 Joshi_et_al_2023 Public

    Analysis code for Joshi et al 2023 Dynamic synchronization between hippocampal representations and stepping

    MATLAB 1

Repositories

Showing 10 of 37 repositories