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3. Overview of datasets

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mayofaulkner edited this page Jan 16, 2021 · 2 revisions

Below is an overview of the input and output datasets used by the ephys alignment GUI. For information about how to prepare your data in this format please see the Preparing data for ephys GUI section

Input Ephys Data

spikes.amps

  • Units: V
  • Type: double
  • Dimensions: [number of spikes]
  • Format: npy
  • Description: Amplitude of each spike.

spikes.clusters

  • Units: index
  • Type: int
  • Dimensions: [number of spikes]
  • Format: npy
  • Description: Cluster assignments for each spike (integers counting from 0). Can be used as direct indexing of the cluster.* attributes

spikes.depths

  • Units: um
  • Type: double
  • Dimensions: [number of spikes]
  • Format: npy
  • Description: Depth along probe of each spike (µm; computed from waveform center of mass). 0 means probe tip, positive upwards.

spikes.times

  • Units: seconds
  • Type: float64
  • Dimensions: [number of spikes]
  • Format: npy
  • Description: Times of spikes (seconds, relative to experiment onset).

clusters.metrics

  • Units: N/A
  • Type: N/A
  • Dimensions: [number of clusters]
  • Format: csv or pqt
  • Description: Quality control metrics at the cluster level. Fields may vary but mandatory field is ks2_label

clusters.peakToTrough

  • Units: ms
  • Type: double
  • Dimensions: [number of clusters]
  • Format: npy
  • Description: Template waveform duration for the cluster. The duration is the time elapsed from peak to through (peak_sample - trough_sample). Value can be negative if peak happens first.

clusters.waveforms

  • Units: V
  • Type: single
  • Dimensions: [number of clusters, number of time samples, number of selected channels]
  • Format: npy
  • Description: Waveform from spike sorting templates (stored as a sparse array, only for a subset of channels closest to the peak channel).

channels.localCoordinates

  • Units: index
  • Type: float
  • Dimensions: [number of channels, 2]
  • Format: npy
  • Description: position of channels relative to probe coordinate system (µm): x (first) dimension is on the width of the shank while (y) is the depth where 0 is the deepest site, and positive above this.

channels.rawInd

  • Units: index
  • Type: int
  • Dimensions: [number of channels]
  • Format: npy
  • Description: array of integers saying which index in the raw recording file (of its home probe) that the channel corresponds to (counting from zero). Can be used as direct indexing for the raw binary files (AP and LF).

_iblqc_ephysSpectralDensityLF.power

  • Units: V**2/Hz
  • Type: float32
  • Dimensions: [number of frequencies, number of channels]
  • Format: npy
  • Description: Power Spectral Density for all channels of LFP band of raw data.

_iblqc_ephysSpectralDensityLF.freqs

  • Units: Hz
  • Type: float32
  • Dimensions: [number of frequencies]
  • Format: npy
  • Description: Frequencies used to compute the power spectral density.

_iblqc_ephysTimeRmsAP.rms

  • Units: V
  • Type: float32
  • Dimensions: [number of time windows, number of channels]
  • Format: npy
  • Description: RMS amplitude of AP band of raw data as a function of time.

_iblqc_ephysTimeRmsAP.timestamps

  • Units: s
  • Type: float32
  • Dimensions: [number of time windows]
  • Format: npy
  • Description: Time scale for the RMS amplitude as a function of time, relative to the raw binary ephys file.

_iblqc_ephysTimeRmsLF.rms

  • Units: V
  • Type: float32
  • Dimensions: [number of time windows, number of channels]
  • Format: npy
  • Description: RMS amplitude of LFP band of raw data as a function of time.

_iblqc_ephysTimeRmsLF.timestamps

  • Units: s
  • Type: float32
  • Dimensions: [number of time windows]
  • Format: npy
  • Description: Time scale for the RMS amplitude as a function of time, relative to the raw binary ephys file.

Input Histology Data

annotation_25

  • Units: NA
  • Type: NA
  • Dimensions: [voxels in AP (528), voxels in DV (320), voxels in ML (456)]
  • Format: nrrd
  • Description: Allen CCF 2017 25 um annotation

average_template_25

  • Units: NA
  • Type: NA
  • Dimensions: [voxels in AP (528), voxels in DV (320), voxels in ML (456)]
  • Format: nrrd
  • Description: Allen CCF 25 um average template

histology_image_GR (optional)

  • Units: NA
  • Type: NA
  • Dimensions: [voxels in ML, voxels in DV, voxels in AP] for tif [voxels in AP, voxels in DV, voxels in ML] for nrrd
  • Format: tif or nrrd
  • Description: Green channel of histology stack registered to 25 um Allen Atlas

histology_image_RD (optional)

  • Units: NA
  • Type: NA
  • Dimensions: [voxels in ML, voxels in DV, voxels in AP] for tif [voxels in AP, voxels in DV, voxels in ML] for nrrd
  • Format: tif or nrrd
  • Description: Red channel of histology stack registered to 25 um Allen Atlas

xyz_picks

  • Units: um
  • Type: double
  • Dimensions: [number of selected points, 3]
  • Format: json
  • Description: Coordinates of selected points along traced probe track with respect to bregma
  • Example content: {"xyz_picks": [[-2863, -3999, -643], [-2813, -3975, -842], [-2788, -4025, -1193], [-2763, -3949, -1543], [-2688, -4025, -1718], ...]}

Output Data

channel_locations

  • Units: NA
  • Type: NA
  • Dimensions: [number of channels]
  • Format: json
  • Description: Information about location of each channel, including x, y and z coordinate with respect to bregma, and brain region in which channel is located
  • Example content:
{
  "channel_0": {
    "x": -2453.8710675786924,
    "y": -4189.7375279160615,
    "z": -3415.687639580306,
    "axial": 20.0,
    "lateral": 43.0,
    "brain_region_id": 0,
    "brain_region": "void"
  },
  "channel_1": {
    "x": -2453.8710675786924,
    "y": -4189.7375279160615,
    "z": -3415.687639580306,
    "axial": 20.0,
    "lateral": 11.0,
    "brain_region_id": 0,
    "brain_region": "void"
  }, 
... 
}

prev_alignments

  • Units: NA
  • Type: NA
  • Dimensions: [number of previous alignments]
  • Format: json
  • Description: Location of reference lines used to align electrophysiology and histology features
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