McNaughton lab ephys data analysis.

ORDER
extractWfAcgMetrics.m -> postProcessKs2.py -> plotPooledMetrics.py -> analyzeBehavFinal.py -> plotBehaviorAll.py -> mainRatemaps.py

Note that many of these scripts are modified from different sources such as Allen Institute, IBL, cortex-lab, Intan, NWB, etc. I've tried to give credit whenever possible.

• APHistology_RS:

  • demo_histology_pipeline_RS.m: main script to begin histology alignment with UCLA silicon probe data modified from https://github.com/petersaj/AP_histology

• preprocessingKs2:

  • IntanRhdToNWB.py: use rhdtonwb-SWIL.py script as a template for converting Intan RHD files to NWB data format
  • ProcessRhd: used to convert Intan RHD files to merged binary files (for Kilosort) after shift alignment, and extract merged 30x sub-sampled LFP, digital, and analog signals
  • rhd_to_bin: optimized version of ProcessRhd by Rob bain to create merged binary files for raw data, sub-sampled lfp file, analog, and digital signals

• postprocessingKs2: scripts for post-processing after spike-sorting and manual curation using Kilsort and Phy

  • utilsClusterQual.py: functions for cluster quality metrics (ISI violations, presence ratio, amplitude cutoff, firing rate threshold)
  • utilsWaveformMetrics.py: functions for calculating waveform metrics (amplitude, peak-to-trough, repolarization slope, spread)
  • postProcessKs2.py: functions for running postprocess kilosort quality checks and saving final processed metrics
  • extractWfAcgMetrics.m: matlab script based on CellExplorer (Petersen et al., 2021) to extract waveform and autocorrelogram metrics
  • plotPooledMetrics.py: script to save pooled unit metrics for all animals and save waveform metrics figure for putative excitatory & inhibitory neuron

• Behavior: scripts for SWIL behavior data analysis

  • behavutils.py: supplement utils for processing behavior .mat file output from smoothwalk
  • analyzeBehavFinal.py: file to process SWIL behavior data and save npy with behavior for each environments and aligned intan timestamps
  • plotBehaviorAll.py: plot speed across all VR environments pooled across all animals

• LFP: scripts for SWIL lfp data analysis

  • decimateLFP_fs24.py.py: script to decimate LFPs by 24x for all recorded channels
  • mea.py: script with utils functions
  • detect_peaks.npy: script to detect peaks (similar to matlab)
  • proCSD.py: run CSD analysis on Si electrodes
  • relLFPPowerByDepth.py: relative power in high-freq band (>300 Hz) by depth

• Ratemaps : scripts for generating rate for SWIL project

  • rmaputils.py: utils for generating ratemaps
  • mainRatemaps.py: file to generate and store ratemaps and save processed data