Using the generated data

The generated templates and recordings can be easily loaded using the MEArec API.

import MEArec as mr

# load recordings
tempgen = mr.load_templates('path-to-templates.h5')

# load recordings
recgen = mr.load_recordings('path-to-recording.h5')

The tempgen is a TemplateGenerator objects and contains the following fields:

  • templates: numpy array with (n_templates, n_electrodes, n_points) - not drifting - or (n_templates, n_drift_steps, n_electrodes, n_points) for drifting ones
  • locations: (n_templates) 3D locations for the templates (for not drifting) or (n_templates, n_drift_steps) 3D locations for drifting templates.
  • rotations: (n_templates) 3D rotations applied to the cell model before computing the template (for drifting templates rotation is fixed)
  • celltypes: (n_templates) cell types of the generated templates
  • info: dictionary with parameters used

The recgen is a RecordingGenerator objects and contains the following fields:

  • recordings: (n_electrodes, n_samples) recordings
  • spiketrains: list of (n_spiketrains) neo.Spiketrain objects
  • templates: (n_spiketrains, n_electrodes, n_templates samples) templates
  • templates_celltypes: (n_spiketrains) templates cell type
  • templates_locations: (n_spiketrains, 3) templates soma locations
  • templates_rotations: (n_spiketrains, 3) 3d model rotations
  • channel_positions: (n_electrodes, 3) electrodes 3D positions
  • timestamps: (n_samples) timestamps in seconds (quantities)
  • voltage_peaks: (n_spiketrains, n_electrodes) average voltage peaks on the electrodes
  • spike_traces: (n_spiketrains, n_samples) clean spike trace for each spike train
  • info: dictionary with parameters used

There are several notebooks available here that show MEArec applications.

Plotting

MEArec contains several plotting routines to facilitate data inspection. For example, a RecordingGenerator object can be plotted as follows:

mr.plot_recordings(recgen)
_images/recordings_static.png

Similarly, templates can be plotted with the plot_templates function. This function also allows to plot drifting templates:

# load drifting templates
tempgen = mr.load_recordings('path-to-drifting-template.h5')
# drifting templates can be plotted one at a time
mr.plot_templates(tempgen, template_ids=100, drifting=True, cmap='Reds)
_images/templates_drift.png

Integration with SpikeInterface

MEArec is designed to help validating spike sorting algorithms. Hence, its integration with the SpikeInterface project, a Python framework for spike sorting analysis, comparison, and validation, is extremely straightforward.

After installing the spikeinterface package, one can easily load a MEArec generated recording, run several spike sorting algorithms, and compare/validate their output:

import spikeinterface.extractors as se
import spikeinterface.sorters as ss
import spikeinterface.comparison as sc

# load recordings and spiketrains with MEArecExtractors
recording = se.MEArecRecordingExtractor('path-to-recording.h5')
sorting_GT = se.MEArecSortingExtractor('path-to-recording.h5')

# run spike sorting
sorting_MS4 = ss.mountainsort4(recording)
sorting_KS = ss.kilosort(recording)

# compare results to ground-truth
comp_MS = sc.compare_sorter_to_ground_truth(sorting_GT, sorting_MS4)
comp_KS = sc.compare_sorter_to_ground_truth(sorting_GT, sorting_MS4)

# get performance
comp_MS.get_performance()
comp_KS.get_performance()

More information about the SpikeInterface framework in the docs and the manuscript.