/myphdlib

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myphdlib

This is a collection of scientific software and analysis documentation that was written during my graduate research.

Datasets

The processed data for each session is stored in an H5 file named output.hdf. Within this file, there are datasets grouped by the associated data processing step.

Stimulus

These datasets contain data associated with the visual stimuli presented during the recordings.

Binary noise

  • stimuli/bn/hr/hf/fields
  • stimuli/bn/hr/hf/grids
  • stimuli/bn/hr/hf/length
  • stimuli/bn/hr/hf/missing
  • stimuli/bn/hr/hf/timestamps
  • stimuli/bn/hr/lf/fields
  • stimuli/bn/hr/lf/grids
  • stimuli/bn/hr/lf/length
  • stimuli/bn/hr/lf/missing
  • stimuli/bn/hr/lf/timestamps
  • stimuli/bn/lr/hf/fields
  • stimuli/bn/lr/hf/grids
  • stimuli/bn/lr/hf/length
  • stimuli/bn/lr/hf/missing
  • stimuli/bn/lr/hf/timestamps
  • stimuli/bn/lr/lf/fields
  • stimuli/bn/lr/lf/grids
  • stimuli/bn/lr/lf/length
  • stimuli/bn/lr/lf/missing
  • stimuli/bn/lr/lf/timestamps

Drifting grating

  • stimuli/dg/grating/motion - (1 x N blocks, int) Direction of grating motion for each block (-1 = CCW, +1 = CW)
  • stimuli/dg/grating/timestamps - (1 x N blocks, float) Timestamp for the beginning of each block
  • stimuli/dg/iti/timestamps - (1 x N blocks, float) Timestamp for the end of each block
  • stimuli/dg/motion/timestamps - (1 x N blocks, float) Timestamp for the onset of grating motion for each block
  • stimuli/dg/probe/contrast - (1 x N trials, float) Probe contrast
  • stimuli/dg/probe/direction - (1 x N trials, int) Direction of the closest saccade for each probe stimulus
  • stimuli/dg/probe/tts - (1 x N trials, float) Latency from closest saccade to each probe (Time to saccade)
  • stimuli/dg/probe/motion - (1 x N trials, int) Direction of grating motion during each probe stimulus
  • stimuli/dg/probe/phase - (1 x N trials, float) Phase of the grating on the first frame of the probe stimulus
  • stimuli/dg/probe/timestamps - (1 x N trials, float) Timestamp for each probe stimulus

Fictive saccades

  • stimuli/fs/coincident
  • stimuli/fs/probes/timestamps
  • stimuli/fs/saccades/timestamps

Moving bars

  • stimuli/mb/offset/timestamps - (1 x N trials, float) - Timestamp for the offset of the moving bars
  • stimuli/mb/onset/timestamps - (1 x N trials, float) - Timestamp for the onset of the moving bars
  • stimuli/mb/orientation - (1 x N trials, float) - Orientation of the moving bars

Sparse noise

  • stimuli/sn/pre/coords - (N trials x 2, float) - Coordinates for the active subregion on each trial (in degrees of visual angle)
  • stimuli/sn/pre/fields - (N trials x H x W, int) - Stimulus presented for each trial
  • stimuli/sn/pre/missing - (1 x N trials, bool) - Boolean mask which identifies misssing trials
  • stimuli/sn/pre/signs - (1 x N trials, bool) - Sign of the stimulus (ON or OFF) for each trial
  • stimuli/sn/pre/timestamps - (1 x N trials) - Timestamp for each trials
  • stimuli/sn/post/coords - (N trials x 2, float) - Coordinates for the active subregion on each trial (in degrees of visual angle)
  • stimuli/sn/post/fields - (N trials x H x W, int) - Stimulus presented for each trial
  • stimuli/sn/post/missing - (1 x N trials, bool) - Boolean mask which identifies misssing trials
  • stimuli/sn/post/signs - (1 x N trials, bool) - Sign of the stimulus (ON or OFF) for each trial
  • stimuli/sn/post/timestamps - (1 x N trials) - Timestamp for each trials

Population

These datasets map directly on to each unit in the extracellular recording.

Masks

  • population/masks/hq - (1 x N units, bool) Units that meet or exceed spike sorting quality metric thresholds
  • population/masks/sr - (1 x N units, bool) Units classified as saccade-related
  • population/masks/vr - (1 x N units, bool) Units classified as visually responsive

Metrics

For spike-sorting quality metrics, the following thresholds were used to delimit low- and high-quality units: Presence ration > 0.9, Refractory period violation rate < 0.5, and Amplitude cutoff < 0.1. Units must meet or exceed all three thresholds to be considered "high-quality."

  • population/metrics/ac - (1 x N units, float) Amplitude cutoff
  • population/metrics/vra/left - (1 x N units, float) Visual response amplitude for probes during leftward motion (in standard deviations)
  • population/metrics/vra/right - (1 x N units, float) Visual response amplitude for probes during rightward motion (in standard deviations)
  • population/metrics/pr - (1 x N units, float) Presence ratio
  • population/metrics/rpvr - (1 x N units, float) Refractory period violation rate
  • population/metrics/ksl - (1 x N units, int) Unit classification assigned by Kilosort (0=mult-unit, 1=single-unit)

ZETA test

ZETA-test p-values and latency to peak response computed for probe stimuli (left and right) and saccades (nasal and temporal).

  • population/zeta/probe/left/latency - (1 x N units, float) Latency from probe onset to peak firing rate (grating moving CCW)
  • population/zeta/probe/left/p - (1 x N units, float) ZETA test p-values looking at activity related to visual probes (grating moving CCW)
  • population/zeta/probe/right/latency - (1 x N units, float) Latency from probe onset to peak firing rate (grating moving CW)
  • population/zeta/probe/right/p - (1 x N units, float) ZETA test p-values looking at activity related to visual probes (grating moving CW)
  • population/zeta/saccade/nasal/latency - (1 x N units, float) Latency from saccade onset to peak firing rate (Nasal saccades)
  • population/zeta/saccade/nasal/p - (1 x N units, float) ZETA test p-values looking at activity related to saccades (Nasal saccades)
  • population/zeta/saccade/temporal/latency - (1 x N units, float) Latency from saccade onset to peak firing rate (Temporal saccades)
  • population/zeta/saccade/temporal/p - (1 x N units, float) ZETA test p-values looking at activity related to saccades (Temporal saccades)