Link

Hippocampal and spatial metrics

Hippocampal and spatial metrics depends on specific files and metadata to be processed the pipeline.

Table of contents

  1. Theta metrics
  2. Spatial metrics
  3. Deep-superficial metrics

Theta metrics

A theta-band filtered time series is generated from the lfp file. Continues theta power and phase is then calculated from the generated time series. For each unit the average theta firing profile is calculated together with the theta phase peak/trough and the strength of the theta entrainment. Learn more about theta oscillation metrics. The tracking file is used for filtering by a minimum running speed.

FilesDescription
sessionName.lfpLFP file
sessionName.InstantaneousTheta.channelInfo.mattheta filtered channel
sessionName.animal.behavior.matbehavioral tracking file
Metadata parameterDescription
session.channelTags.Theta.channelsTheta channel tag (required)

Spatial metrics

All spatial metrics are generated from an existing 1D firing rate map. Learn more about spatial metrics and the firing rate map Matlab struct.

FilesDescription
firingRateMaps.firingRateMap.mat1D firing rate map

Deep-superficial metrics

Deep-superficial metrics are calculated from ripple timestamps and the average ripple is extracted from a channel from the lfp file. A reveral point for the polarity of the sharp wave is derived from a time interval before the average ripple, aligned to their peaks. Deep-superficial distance is estimmated from the reversal point by assigning a numeric value determined from the channel offset to the reversal point.

Learn more about deep-superficial metrics, and see the tutorial here.

FilesDescription
sessionName.lfpLFP file (generated in the processing module)
sessionName.ripples.events.matRipples events (generated in the processing module)
‘sessionName.deepSuperficialfromRipple.channelinfo.mat’Ripples events (generated in the processing module)
Metadata parameterDescription
session.channelTags.Ripple.channelsRipple channel tag (required)
session.analysisTags.probesLayoutRipple channel tag (required; linear,staggered,poly2, edge,poly3,poly5)
session.analysisTags.probesVerticalSpacingVertical spacing between sites (required, [µm])
session.channelTags.Bad.channelsBad channels
session.channelTags.Bad.electrodeGroupsBad electrode groups (e.g. broken shanks)
session.channelTags.Cortical.electrodeGroupsCortical spike groups