Neural and behavioral data from: A dynamic sequence of visual processing initiated by gaze shifts

# A dynamic sequence of visual processing initiated by gaze shifts [Access this dataset on Dryad](https://doi.org/10.5061/dryad.kd51c5bck) For a detailed description of experimental and analysis methods, see the publication: Parker PRL, Martins DM, Leonard ESP, Casey NM, Sharp SL, Abe ETT, Smear MC, Yates JL, Mitchell JF, & Niell CM. (2023). *Nature Neuroscience.* A dynamic sequence of visual processing initiated by gaze shifts. ## Data and file structure The data are formatted as a single HDF5 file. The file contains four groups of experiments: 1. Head-fixed / freely moving mice ("hffm.h5") 2. Freely moving mice in the light vs. dark ("ltdk.h5") 3. Head-fixed flashed stimuli ("hffl.h5") 4. Freely gazing marmosets ("marm.h5") ### Mouse data These keys are used in "hffm.h5", "ltdk.h5" and "hffl.h5". #### Keys across stimuli | Name | Type | Shape | Description | | ---- | ---- | ----- | ----------- | | `_index` | `int` | () | Origional index of the unit in the dataframe | | `session` | `str` | () | Session name, e.g., '010101_NAME_CONDITION_RIG' | | `Probe_channel` | `int64` | () | Probe channel number | | `Probe_shank` | `int64` | () | Which shank of the probe the cell was recorded from. | | `Phy2_label` | `str` | () | 'good', 'mua' (multi-unit activity) or 'noise' labels from Phy2. | | `Spike_waveform` | `list` | (61,) | Spike waveform. | | `Afterhyperpolarization` | `np.float` | () | Afterhyperpolarization amplitude. | | `Putative_cell_type` | `str` | () | Putative cell type, based on waveform shape, either 'exc' for excitatory or 'inh' for inhibitory. | | `best_ellipse_fit_m` | `np.float` | () | Best fit ellipse fit slope. | | `best_ellipse_fit_r` | `np.float` | () | Best fit ellipse fit r2. | | `dsi_for_sf_pref` | `np.float` | () | Direction selectivity index for the preferred spatial frequency. | | `fires_2sp_sec` | `np.float` | () | Firing rate during gaze shifts. | | `gazecluster` | `np.float` | () | Cluster label for gaze shifts. | | `gazeshift_DSI` | `np.float` | () | Direction selectivity index for gaze shifts. | | `gazeshift_responsive` | `np.float` | () | Whether or not the cell was responsive during gaze shifts. | | `grat_psth_drop` | `np.float` | () | Drop in firing rate during gratings. | | `grat_speed_dps` | `np.float` | () | Speed of the gratings in deg/sec. | | `has_dark` | `bool` | () | Whether or not the recording has a freely moving dark stimulus. | | `has_hf` | `bool` | () | Whether or not the recording has a head-fixed stimulus. | | `has_optic_flow` | `bool` | () | Whether or not the recording has an optic flow stimulus. | | `index` | `int` | () | Index of the unit in the dataframe | | `mod_at_pref_peak` | `np.float` | () | Modulation at the preferred peak. | | `movement_responsive` | `np.float` | () | Whether or not the cell was responsive during movement. | | `nonpref_comp_psth` | `np.ndarray` | (2001,) | Non-preferred component PSTH. | | `nonpref_comp_psth_FmDk` | `np.ndarray` | (2001,) | Non-preferred component PSTH, aligned to the start of the dark stimulus. | | `nonpref_comp_psth_raw` | `np.ndarray` | (2001,) | Non-preferred component PSTH, aligned to the start of the dark stimulus, without correcting for drift and offset in data aquisition. | | `nonpref_gazeshift_direction` | `np.float` | () | Non-preferred gaze shift direction. | | `nonpref_gazeshift_psth` | `np.ndarray` | (2001,) | Non-preferred gaze shift PSTH. | | `nonpref_gazeshift_psth_FmDk` | `np.ndarray` | (2001,) | Non-preferred gaze shift PSTH, aligned to the start of the dark stimulus. | | `nonpref_gazeshift_psth_raw` | `np.ndarray` | (2001,) | Non-preferred gaze shift PSTH, aligned to the start of the dark stimulus, without correcting for drift and offset in data aquisition. | | `norm_gratings_psth` | `np.ndarray` | (2001,) | Normalized gratings PSTH. | | `norm_mod_at_pref_peak` | `float` | () | Normalized modulation at the preferred direction's peak. | | `norm_mod_for_Gt` | `float` | () | Normalized modulation for gratings. | | `norm_mod_for_Rc` | `float` | () | Normalized modulation for reversing checkerboard. | | `norm_mod_for_Sn` | `float` | () | Normalized modulation for sparse noise. | | `norm_ori_tuning_high` | `np.array` | (8,) | High spatial frequency orientation tuning curve. | | `norm_ori_tuning_low` | `np.array` | (8,) | Low spatial frequency orientation tuning curve. | | `norm_ori_tuning_mid` | `np.array` | (8,) | Mid spatial frequency orientation tuning curve. | | `norm_waveform` | `np.ndarray` | (61,) | Normalized waveform. | | `osi_for_sf_pref` | `float` | () | Orientation selectivity index for the preferred spatial frequency. | | `pref_comp_direction` | `str` | () | Preferred component direction. | | `pref_comp_psth` | `np.ndarray` | (2001,) | Preferred component PSTH. | | `pref_comp_psth_FmDk` | `np.ndarray` | (2001,) | Preferred component PSTH, aligned to the start of the dark stimulus. | | `pref_comp_psth_raw` | `np.ndarray` | (2001,) | Preferred component PSTH, aligned to the start of the dark stimulus, without correcting for drift and offset in data aquisition. | | `pref_gazeshift_direction` | `str` | () | Preferred gaze shift direction. | | `pref_gazeshift_psth` | `np.ndarray` | (2001,) | Preferred gaze shift PSTH. | | `pref_gazeshift_psth_FmDk` | `np.ndarray` | (2001,) | Preferred gaze shift PSTH, aligned to the start of the dark stimulus. | | `pref_gazeshift_psth_for_kmeans` | `np.ndarray` | (2001,) | Preferred gaze shift PSTH for k-means clustering, with unresponsive cells set to array of zeros to seed unresponsive cluster. | | `pref_gazeshift_psth_raw` | `np.ndarray` | (2001,) | Gaze shift PSTH in the preferred direction, not normalized. | | `pref_intersacc_psth` | `np.ndarray` | (2001,) | Preferred intersaccade PSTH. | | `pref_psth_baseline_slope` | `np.float` | () | Slope of the baseline firing rate during the preferred direction of gaze shifts. | | `probe_name` | `str` | Model of ephys probe used. | | `raw_mod_at_pref_peak` | `np.float` | () | Raw modulation at the preferred direction's peak. | | `raw_mod_for_Gt` | `np.float` | () | Raw modulation for gratings. | | `raw_mod_for_Rc` | `np.float` | () | Raw modulation for reversing checkerboard. | | `raw_mod_for_Sn` | `np.float` | () | Raw modulation for sparse noise. | | `responsive_to_contrast` | `bool` | () | Whether or not the cell was responsive to contrast. | | `responsive_to_gratings` | `bool` | () | Whether or not the cell was responsive to gratings. | | `sf_pref_cpd` | `np.float` | () | Spatial frequency preference in cycles per degree. | | `t0` | `np.float` | () | Time of the first spike across merged recordings. | | `tf_pref_cps` | `np.float` | () | Temporal frequency preference in cycles per second. | | `use_in_dark_analysis` | `bool` | () | Whether or not the cell was used in the dark analysis. | | `use_in_optic_flow` | `bool` | () | Whether or not the cell was used in the optic flow analysis. | | `waveform_km_label` | `int` | () | K-means cluster label for waveform. | | `waveform_trough_width` | `np.float` | () | Width of the trough of the waveform. | #### Freely moving condition | Name | Type | Shape | Description | | ---- | ---- | ----- | ----------- | | `FmLt_n_spikes` | `int64` | () | Number of spikes in the recording. | | `FmLt_t0` | `float64` | () | Time of the first spike, in units of seconds. This is the time of day, and used to align recordings. | | `FmLt_imuT` | `ndarray` | (N,) | IMU timestamps relative to `FmLt_t0`. Values from before the first ephys spike are negative. | | `FmLt_eyeT` | `ndarray` | (N,) | Eye camera timestamps relative to `FmLt_t0`. Values from before the first ephys spike are negative. | | `FmLt_topT` | `ndarray` | (N, ) | Topdown camera timerstamps relative to `FmLt_t0`. Values before the first ephys spike are negative. | | `FmLt_worldT` | `ndarray` | (N,) | World camera timestamps relative to `FmLt_t0`. Values from before the first ephys spike are negative. | | `FmLt_spikeT` | `ndarray` | (n_spikes,) | Spike times, in units of seconds. | | `FmLt_spikeTraw` | `list` | (n_spikes,) | Spike times, in units of seconds. This is without correcting the drift and offset in data aquisition. | | `FmLt_rate` | `ndarray` | (`len(modelT)`,) | Spike rate for all stimuli in sp/s and aligned to `FmLT_modelT` | | `FmLt_gyro_x` | `ndarray` | (`len(imuT)`,) | IMU x gyro data. | | `FmLt_gyro_y` | `ndarray` | (`len(imuT)`,) | IMU y gyro data. | | `FmLt_gyro_z` | `ndarray` | (`len(imuT)`,) | IMU z gyro data. | | `FmLt_roll` | `ndarray` | (`len(imuT)`,) | Roll of head orientation at each time point, in units of deg. | | `FmLt_pitch` | `ndarray` | (`len(imuT)`,) | Pitch of head orientation at each time point, in units of deg. | | `FmLt_dHead` | `ndarray` | (`len(eyeT)`,) | Head velocity in the z-axis. | | `FmLt_theta` | `ndarray` | (`len(eyeT)`,) | Horizontal eye position in deg. Length N is `len(FmLt_imuT)` | | `FmLt_phi` | `ndarray` | (`len(eyeT)`,) | Vertical eye position in deg. | | `FmLt_dEye` | `ndarray` | (`len(eyeT)-1`,) | Horizontal eye velocity in deg/sec. | | `FmLt_dEye_dpf` | `ndarray` | (`len(eyeT)-1`,) | Horizontal eye velocity in deg/frame. | | `FmLt_dGaze` | `ndarray` | (`len(eyeT)-1`) | Horizontal gaze velcocity in deg/sec, where gaze is defined as dEye + dHead. | | `FmLt_head_yaw` | `ndarray` | (`len(topT)`,) | Head yaw in deg, from the topdown camera. Calculated as the line tangent to the angle between its ears. 0 deg is the rightwards horizontal in the view of the topdown camera. | | `FmLt_body_yaw` | `ndarray` | (`len(topT)`,) | Body yaw in deg, from the topdown camera. Calculated as the angle between its neck and the base of its tail. 0 deg is the rightwards horizontal in the view of the topdown camera. | | `FmLt_movement_vector_yaw` | `ndarray` | (`len(topT)`,) | Movement yaw in deg, from the topdown camera. Calculated as the angle between its velocity vector and the horizontal. 0 deg is the rightwards horizontal in the view of the topdown camera. | | `FmLt_saccade_rightPSTH` | `ndarray` | (2001,) | PSTH for rightward saccades. | | `FmLt_saccade_leftPSTH` | `ndarray` | (2001,) | PSTH for leftward saccades. | | `FmLt_compensatory_right_saccPSTH` | `ndarray` | (2001,) | PSTH for rightwards compensatory eye/head movements. | | `FmLt_compensatory_left_saccPSTH` | `ndarray` | (2001,) | PSTH for leftwards compensatory eye/head movements. | | `FmLt_gazeshift_left_saccPSTH` | `ndarray` | (2001,) | PSTH for leftwards gaze shifts. | | `FmLt_gazeshift_right_saccPSTH` | `ndarray` | (2001,) | PSTH for rightwards gaze shifts. | | `FmLt_saccade_right_saccT` | `ndarray` | (N,) | Saccade times to the right for all eye/head movements. Size N is the number of this type of eye movement that happened during the recording. | | `FmLt_saccade_left_saccT` | `ndarray` | (N,) | Saccade times to the left for all eye/head movements. Size N is the number of this type of eye movement that happened during the recording. | | `FmLt_compensatory_righ_sacc_T` | `ndarray` | (N,) | Rightwards compensatory eye/head movemement times. Size N is the number of this type of eye movement that happened during the recording. | | `FmLt_compensatory_left_saccT` | `ndarray` | (N,) | Leftwards compensatory eye/head movemement times. Size N is the number of this type of eye movement that happened during the recording. | | `FmLt_gazeshift_left_saccT` | `ndarray` | (N,) | Leftwards gaze shift times. Size N is the number of this type of eye movement that happened during the recording. | | `FmLt_gazeshift_right_saccT` | `ndarray` | (N,) | Rightwards gaze shift times. Size N is the number of this type of eye movement that happened during the recording. | | `FmLt_spike_triggered_average` | `ndarray` | (60, 80) | Spike triggered average. | | `FmLt_spike_triggered_variance` | `ndarray` | (60, 80) | Spike triggered variance. | | `FmLt_contrast_tuning_bins` | `ndarray` | (11,) | Contrast tuning curve bins. Each of these is the bin center (not the edge.) | | `FmLt_contrast_tuning` | `ndarray` | (11,) | Contrast tuning curve. | | `FmLt_contrast_tuning_err` | `ndarray` | (11,) | Contrast tuning curve error at each bin. | | `FmLt_pupilradius_tuning_bins` | `ndarray` | (9,) | Pupil radius tuning curve bins. Each of these is the bin center (not the edge). | | `FmLt_pupilradius_tuning` | `ndarray` | (9,) | Pupil radius tuning curve. | | `FmLt_pupilradius_tuning_err` | `ndarray` | (9,) | Pupil radius tuning curve error at each bin. | | `FmLt_theta_tuning_bins` | `ndarray` | (9,) | Theta tuning curve bins. Each of these is the bin center (not the edge). | | `FmLt_theta_tuning` | `ndarray` | (9,) | Theta tuning curve. | | `FmLt_theta_tuning_err` | `ndarray` | (9,) | Theta tuning curve error at each bin. | | `FmLt_phi_tuning_bins` | `ndarray` | (9,) | Phi tuning curve bins. Each of these is the bin center (not the edge). | | `FmLt_phi_tuning` | `ndarray` | (9,) | Phi tuning curve. | | `FmLt_phi_tuning_err` | `ndarray` | (9,) | Phi tuning curve error at each bin. | | `FmLt_gyrox_tuning_bins` | `ndarray` | (9,) | Gyro x tuning curve bins. Each of these is the bin center (not the edge). | | `FmLt_gyrox_tuning` | `ndarray` | (9,) | Gyro x tuning curve. | | `FmLt_gyrox_tuning_err` | `ndarray` | (9,) | Gyro x tuning curve error at each bin. | | `FmLt_gyroy_tuning_bins` | `ndarray` | (9,) | Gyro y tuning curve bins. Each of these is the bin center (not the edge). | | `FmLt_gyroy_tuning` | `ndarray` | (9,) | Gyro y tuning curve. | | `FmLt_gyroy_tuning_err` | `ndarray` | (9,) | Gyro y tuning curve error at each bin. | | `FmLt_gyroz_tuning_bins` | `ndarray` | (9,) | Gyro z tuning curve bins. Each of these is the bin center (not the edge). | | `FmLt_gyroz_tuning` | `ndarray` | (9,) | Gyro z tuning curve. | | `FmLt_gyroz_tuning_err` | `ndarray` | (9,) | Gyro z tuning curve error at each bin. | | `FmLt_roll_tuning_bins` | `ndarray` | (9,) | Roll tuning curve bins. Each of these is the bin center (not the edge). | | `FmLt_roll_tuning` | `ndarray` | (9,) | Roll tuning curve. | | `FmLt_roll_tuning_err` | `ndarray` | (9,) | Roll tuning curve error at each bin. | | `FmLt_pitch_tuning_bins` | `ndarray` | (9,) | Pitch tuning curve bins. Each of these is the bin center (not the edge). | | `FmLt_pitch_tuning` | `ndarray` | (9,) | Pitch tuning curve. | | `FmLt_pitch_tuning_err` | `ndarray` | (9,) | Pitch tuning curve error at each bin. | | `FmLt_running_speed` | `ndarray` | (`len(topT)`,) | Speed of the animal from topdown camera, in units of cm/sec. | | `FmLt_is_running_forward` | `ndarray` | (`len(topT)`,) | Bool array of whether or not the animal was running forward, defined as the animal running > 2 cm/sec while oriented so that the direction of locomotion is < +/-40 deg different from the orientation of its body. | | `FmLt_is_running_backward` | `ndarray` | (`len(topT)`,) | Bool array of whether or not the animal was running backward, defined as the animal running > 2 cm/sec while oriented so that the direction of locomotion is > +/-40 deg different from the tangent of the orientation of its body. | | `FmLt_is_fine_motion` | `ndarray` | (`len(topT)`,) | Bool array of whether or not the animal was moving > 2 cm/sec but was not running forward or backward. | | `FmLt_is_stationary` | `ndarray` | (`len(topT)`,) | Bool array of whether or not the animal was not moving < 2 cm/sec, i.e., nearly stationary. | | `FmLt_active_fr` | `float64` | () | Average firing rate during active periods. | | `FmLt_inactive_fr` | `float64` | () | Average firing rate during inactive periods. | | `FmLt_gazeshift_baseline` | `np.array` | (800) | Baseline firing rate during gaze shifts. | | `FmLt_gazeshift_med_baseline` | `np.array` | (800) | Median baseline firing rate during gaze shifts. | | `FmLt_gazeshift_peakT` | `float64` | () | Time of peak firing rate during gaze shifts. | | `FmLt_gazeshift_peak_val` | `float64` | () | Peak firing rate during gaze shifts. | | `FmLt_gazeshift_troughT` | `float64` | () | Time of trough firing rate during gaze shifts. | | `FmLt_gazeshift_zscore` | `float64` | () | Z-score of firing rate during gaze shifts. | | `FmLt_intersacc_left_saccPSTH_dHead1` | `np.array` | (2001) | PSTH for leftwards saccades which are between the criteria for gaze shifts versus compensatory movements. | | `FmLt_intersacc_right_saccPSTH_dHead1` | `np.array` | (2001) | PSTH for rightwards saccades which are between the criteria for gaze shifts versus compensatory movements. | | `FmLt_gyrox_modind` | `float64` | () | Modulation index for gyro x. | | `FmLt_gyroy_modind` | `float64` | () | Modulation index for gyro y. | | `FmLt_gyroz_modind` | `float64` | () | Modulation index for gyro z. | | `FmLt_pitch_modind` | `float64` | () | Modulation index for pitch. | | `FmLt_roll_modind` | `float64` | () | Modulation index for roll. | | `FmLt_theta_modind` | `float64` | () | Modulation index for theta. | | `FmLt_phi_modind` | `float64` | () | Modulation index for phi. | | `Fm_fr` | `float64` | () | Average firing rate. | #### Gratings stimulus | Name | Type | Shape | Description | | ---- | ---- | ----- | ----------- | | `Gt_PSTH` | `np.array` | (3001,) | PSTH for onset of gratings stimulus. | | `Gt_ballspeed` | `np.array` | (`len(ballT)`,) | Treadmill speed, in units of cm/sec. | | `Gt_ballspeed_tuning_bins` | `np.array` | (11,) | Ball speed tuning curve bins. Each of these is the bin center (not the edge). | | `Gt_ballspeed_tuning` | `np.array` | (11,) | Ball speed tuning curve. | | `Gt_ballspeed_tuning_err` | `np.array` | (11,) | Ball speed tuning curve error at each bin. | | `Gt_best_direction` | `float64` | () | Direction of the grating that evoked the highest firing rate. | | `Gt_best_orientation` | `float64` | () | Orientation of the grating that evoked the highest firing rate. | | `Gt_contrast` | `np.array` | (`len(worldT)`,) | Contrast of the stimulus at each time point, aquired through the worldcam. | | `Gt_contrast_tuning_bins` | `np.array` | (11,) | Contrast tuning curve bins. Each of these is the bin center (not the edge.) | | `Gt_contrast_tuning` | `np.array` | (11,) | Contrast tuning curve. | | `Gt_contrast_tuning_err` | `np.array` | (11,) | Contrast tuning curve error at each bin. | | `Gt_dEye` | `np.array` | (`len(eyeT)-1`,) | Eye movement velocity in units of deg/sec. | | `Gt_dEye_dpf` | `np.array` | (`len(eyeT)-1`,) | Eye movement velocity in units of deg/frame. | | `Gt_dsi_high` | `float64` | () | Direction selectivity index for high SF. | | `Gt_dsi_low` | `float64` | () | Direction selectivity index for low SF. | | `Gt_dsi_mid` | `float64` | () | Direction selectivity index for mid SF. | | `Gt_evoked_rate` | `float64` | () | Evoked firing rate during the stimulus. | | `Gt_eyeT` | `np.array` | (`len(eyeT)`,) | Eye camera timestamps relative to `Gt_t0`. Values from before the first ephys spike are negative. | | `Gt_fr` | `float64` | () | Average firing rate. | | `Gt_leftsacc_avg` | `np.array` | (2001,) | Average PSTH for leftward saccades. | | `Gt_n_spikes` | `int64` | () | Number of spikes during all stimuli combined. | | `Gt_norm_PSTH` | `np.array` | (3001,) | Normalized PSTH. | | `Gt_tuning` | `np.array` | (8, 3, 2) | Gratings tuning with shape (orientation, SF, TF). | | `Gt_osi_high` | `float64` | () | Orientation selectivity index for high SF. | | `Gt_osi_low` | `float64` | () | Orientation selectivity index for low SF. | | `Gt_osi_mid` | `float64` | () | Orientation selectivity index for mid SF. | | `Gt_phi` | `np.array` | (`len(eyeT)`,) | Phi position of the head, in units of degrees. | | `Gt_phi_tuning` | `np.array` | (9,) | Phi tuning curve. | | `Gt_phi_tuning_bins` | `np.array` | (9,) | Phi tuning curve bins. Each of these is the bin center (not the edge). | | `Gt_phi_tuning_err` | `np.array` | (9,) | Phi tuning curve error at each bin. | | `Gt_pupilradius_tuning` | `np.array` | (9,) | Pupil radius tuning curve. | | `Gt_pupilradius_tuning_bins` | `np.array` | (9,) | Pupil radius tuning curve bins. Each of these is the bin center (not the edge). | | `Gt_pupilradius_tuning_err` | `np.array` | (9,) | Pupil radius tuning curve error at each bin. | | `Gt_rate` | `np.array` | (N,) | Spike rate for all stimuli interpolated to `modelT`. | | `Gt_responsive` | `bool` | () | Whether or not the cell was responsive to the stimulus. | | `Gt_rightsacc_avg` | `np.array` | (2001,) | Average PSTH for rightward saccades. | | `Gt_spikeT` | `np.array` | (N,) | Spike times, in units of seconds. | | `Gt_spikeTraw` | `list` | (N,) | Spike times, in units of seconds. This is without correcting the drift and offset in data aquisition. | | `Gt_spike_triggered_average` | `np.array` | (60, 80) | Spike triggered average. | | `Gt_spike_triggered_variance` | `np.array` | (60, 80) | Spike triggered variance. | | `Gt_spontaneous_rate` | `float64` | () | Spontaneous firing rate. | | `Gt_theta` | `np.array` | (`len(eyeT)`,) | Theta position of the head, in units of degrees. | | `Gt_theta_tuning` | `np.array` | (9,) | Theta tuning curve. | | `Gt_theta_tuning_bins` | `np.array` | (9,) | Theta tuning curve bins. Each of these is the bin center (not the edge). | | `Gt_theta_tuning_err` | `np.array` | (9,) | Theta tuning curve error at each bin. | #### Reversing checkerboard stimulus | Name | Type | Shape | Description | | ---- | ---- | ----- | ----------- | | `Rc_ballspeed` | `np.array` | (`len(ballT)`,) | Treadmill speed, in units of cm/sec. | | `Rc_ballspeed_tuning_bins` | `np.array` | (11,) | Ball speed tuning curve bins. Each of these is the bin center (not the edge). | | `Rc_ballspeed_tuning` | `np.array` | (11,) | Ball speed tuning curve. | | `Rc_ballspeed_tuning_err` | `np.array` | (11,) | Ball speed tuning curve error at each bin. | | `Rc_ch_center_of_layer_4` | `list` | (2,) or (4,) | Center of layer 4 for each shank. | | `Rc_ch_lfp_relative_depth` | `list` | (2,) or (4,) | Relative depth of each shank in um. | | `Rc_contrast` | `np.array` | (`len(worldT)`,) | Contrast of the stimulus at each time point, aquired through the worldcam. | | `Rc_contrast_tuning` | `np.array` | (11,) | Contrast tuning curve. | | `Rc_contrast_tuning_bins` | `np.array` | (11,) | Contrast tuning curve bins. Each of these is the bin center (not the edge.) | | `Rc_contrast_tuning_err` | `np.array` | (11,) | Contrast tuning curve error at each bin. | | `Rc_current_source_density` | `np.array` | (n_channels, 18000) | Current source density for each shank. | | `Rc_dEye_dpf` | `np.array` | (`len(eyeT)-1`,) | Eye movement velocity in units of deg/frame. | | `Rc_depth_from_layer4` | `float` | () | Depth of the cell from layer 4 in um. | | `Rc_eyeT` | `np.array` | (`len(eyeT)`,) | Eye camera timestamps relative to `Rc_t0`. Values from before the first ephys spike are negative. | | `Rc_fr` | `float64` | () | Average firing rate. | | `Rc_gaze_max_cc` | `float64` | () | Maximum cross correlation between the freely moving gaze shift PSTH and the response to Rc stimulus onset. | | `Rc_layer5cent_from_lfp` | `float` | () | Distance from layer 5 to the center of the LFP shank in um. | | `Rc_leftsacc_avg` | `np.array` | (2001,) | Average PSTH for leftward saccades. | | `Rc_n_spikes` | `float` | () | Number of spikes during all stimuli combined. | | `Rc_norm_PSTH` | `np.array` | (2001,) | Normalized PSTH. | | `Rc_peak_time` | `float64` | () | Time of peak firing rate. | | `Rc_phi` | `np.array` | (`len(eyeT)`,) | Phi position of the head, in units of degrees. | | `Rc_phi_tuning` | `np.array` | (9,) | Phi tuning curve. | | `Rc_phi_tuning_bins` | `np.array` | (9,) | Phi tuning curve bins. Each of these is the bin center (not the edge). | | `Rc_phi_tuning_err` | `np.array` | (9,) | Phi tuning curve error at each bin. | | `Rc_psth` | `np.array` | (2001,) | PSTH for onset of Rc stimulus. | | `Rc_pupilradius_tuning` | `np.array` | (9,) | Pupil radius tuning curve. | | `Rc_pupilradius_tuning_bins` | `np.array` | (9,) | Pupil radius tuning curve bins. Each of these is the bin center (not the edge). | | `Rc_pupilradius_tuning_err` | `np.array` | (9,) | Pupil radius tuning curve error at each bin. | | `Rc_rate` | `np.array` | (N,) | Spike rate for all stimuli interpolated to `modelT`. | | `Rc_relative_depth` | `float` | () | Relative depth of the cell in um. | | `Rc_responsive` | `bool` | () | Whether or not the cell was responsive to the stimulus. | | `Rc_rightsacc_avg` | `np.array` | (2001,) | Average PSTH for rightward saccades. | | `Rc_spikeT` | `np.array` | (N,) | Spike times, in units of seconds. | | `Rc_spikeTraw` | `list` | (N,) | Spike times, in units of seconds. This is without correcting the drift and offset in data aquisition. | | `Rc_spike_triggered_average` | `np.array` | (60, 80) | Spike triggered average. | | `Rc_spike_triggered_variance` | `np.array` | (60, 80) | Spike triggered variance. | | `Rc_theta` | `np.array` | (`len(eyeT)`,) | Theta position of the head, in units of degrees. | | `Rc_theta_tuning` | `np.array` | (9,) | Theta tuning curve. | | `Rc_theta_tuning_bins` | `np.array` | (9,) | Theta tuning curve bins. Each of these is the bin center (not the edge). | | `Rc_theta_tuning_err` | `np.array` | (9,) | Theta tuning curve error at each bin. | | `raw_mod_for_Rc` | `float64` | () | Raw modulation index for Rc stimulus. Only exists for the hffl dataset. | | `norm_mod_for_Rc` | `float64` | () | Normalized modulation index for Rc stimulus. Only exists for the hffl dataset. | #### Sparse noise stimulus | Name | Type | Shape | Description | | ---- | ---- | ----- | ----------- | | `Sn_PSTH` | `np.array` | (2001,) | PSTH for onset of white noise stimulus. | | `Sn_ballspeed` | `np.array` | (`len(ballT)`,) | Treadmill speed, in units of cm/sec. | | `Sn_ballspeed_tuning_bins` | `np.array` | (11,) | Ball speed tuning curve bins. Each of these is the bin center (not the edge). | | `Sn_ballspeed_tuning` | `np.array` | (11,) | Ball speed tuning curve. | | `Sn_ballspeed_tuning_err` | `np.array` | (11,) | Ball speed tuning curve error at each bin. | | `Sn_contrast` | `np.array` | (`len(worldT)`,) | Contrast of the stimulus at each time point, aquired through the worldcam. | | `Sn_contrast_tuning` | `np.array` | (11,) | Contrast tuning curve. | | `Sn_contrast_tuning_bins` | `np.array` | (11,) | Contrast tuning curve bins. Each of these is the bin center (not the edge.) | | `Sn_contrast_tuning_err` | `np.array` | (11,) | Contrast tuning curve error at each bin. | | `Sn_dEye` | `np.array` | (`len(eyeT)-1`,) | Eye movement velocity in units of deg/sec. | | `Sn_dEye_dpf` | `np.array` | (`len(eyeT)-1`,) | Eye movement velocity in units of deg/frame. | | `Sn_eyeT` | `np.array` | (`len(eyeT)`,) | Eye camera timestamps relative to `Sn_t0`. Values from before the first ephys spike are negative. | | `Sn_fr` | `float64` | () | Average firing rate. | | `Sn_gaze_max_cc` | `float64` | () | Maximum cross correlation between the freely moving gaze shift PSTH and the response to Sn stimulus onset. | | `Sn_leftsacc_avg` | `np.array` | (2001,) | Average PSTH for leftward saccades. | | `Sn_n_spikes` | `float` | () | Number of spikes during all stimuli combined. | | `Sn_norm_PSTH` | `np.array` | (2001,) | Normalized PSTH. | | `Sn_peak_time` | `float64` | () | Time of peak firing rate. | | `Sn_phi` | `np.array` | (`len(eyeT)`,) | Phi position of the head, in units of degrees. | | `Sn_phi_tuning` | `np.array` | (9,) | Phi tuning curve. | | `Sn_phi_tuning_bins` | `np.array` | (9,) | Phi tuning curve bins. Each of these is the bin center (not the edge). | | `Sn_phi_tuning_err` | `np.array` | (9,) | Phi tuning curve error at each bin. | | `Sn_pupilradius_tuning` | `np.array` | (9,) | Pupil radius tuning curve. | | `Sn_pupilradius_tuning_bins` | `np.array` | (9,) | Pupil radius tuning curve bins. Each of these is the bin center (not the edge). | | `Sn_pupilradius_tuning_err` | `np.array` | (9,) | Pupil radius tuning curve error at each bin. | | `Sn_rate` | `np.array` | (N,) | Spike rate for all stimuli interpolated to `modelT`. | | `Sn_responsive` | `bool` | () | Whether or not the cell was responsive to the stimulus. | | `Sn_rightsacc_avg` | `np.array` | (2001,) | Average PSTH for rightward saccades. | | `Sn_spikeT` | `np.array` | (N,) | Spike times, in units of seconds. | | `Sn_spikeTraw` | `list` | (N,) | Spike times, in units of seconds. This is without correcting the drift and offset in data aquisition. | | `Sn_spike_triggered_average` | `np.array` | (60, 80) | Spike triggered average. | | `Sn_spike_triggered_variance` | `np.array` | (60, 80) | Spike triggered variance. | | `Sn_theta` | `np.array` | (`len(eyeT)`,) | Theta position of the head, in units of degrees. | | `Sn_theta_tuning` | `np.array` | (9,) | Theta tuning curve. | | `Sn_theta_tuning_bins` | `np.array` | (9,) | Theta tuning curve bins. Each of these is the bin center (not the edge). | | `Sn_theta_tuning_err` | `np.array` | (9,) | Theta tuning curve error at each bin. | | `Sn_Amplitude` | `np.array` | (N,) | Spike amplitude. | | `Sn_ContamPct` | `float64` | () | Spike contamination percentage. | | `Sn_KSLabel` | `str` | () | Spike label. | | `Sn_amp` | `np.array` | (N,) | Spike amplitude. | | `Sn_ch` | `np.array` | (N,) | Spike channel. | | `Sn_depth` | `float` | () | Depth of the cell in um. | | `Sn_group` | `np.array` | (N,) | Spike group. | | `Sn_t0` | `float64` | () | Time of first spike. | | `Sn_waveform` | `np.array` | (N, 48) | Spike waveform. | | `Sn_sh` | `np.array` | (N,) | Spike shank. | | `Sn_saccade_rightT` | `ndarray` | (N,) | Rightwards saccade times. Size N is the number of this type of eye movement that happened during the recording. | | `Sn_saccade_leftT` | `ndarray` | (N,) | Leftwards saccade times. Size N is the number of this type of eye movement that happened during the recording. | | `Sn_saccade_rightPSTH` | `ndarray` | (2001,) | PSTH for rightwards saccades. | | `Sn_saccade_leftPSTH` | `ndarray` | (2001,) | PSTH for leftwards saccades. | | `Sn_worldT` | `np.array` | (`len(worldT)`,) | World camera timestamps relative to `Sn_t0`. Values from before the first ephys spike are negative. | | `Sn_stim_PSTH_onSub_all` | `np.array` | (2001,) | PSTH for the onset of stimulus change where the stimilus on the unit's 'ON' receptive field changed. | | `Sn_stim_PSTH_onSub_darkRF` | `np.array` | (2001,) | PSTH for the onset of stimulus change where the stimilus on the unit's 'ON' receptive field changed to a dark patch. | | `Sn_stim_PSTH_onSub_lightRF` | `np.array` | (2001,) | PSTH for the onset of stimulus change where the stimilus on the unit's 'ON' receptive field changed to a light patch. | | `Sn_stim_PSTH_onSub_bckgndRF` | `np.array` | (2001,) | PSTH for the onset of stimulus change where the stimilus everywhere except the unit's 'ON' receptive field changed. | | `Sn_stim_PSTH_offSub_all` | `np.array` | (2001,) | PSTH for the offset of stimulus change where the stimilus on the unit's 'OFF' receptive field changed. | | `Sn_stim_PSTH_offSub_darkRF` | `np.array` | (2001,) | PSTH for the offset of stimulus change where the stimilus on the unit's 'OFF' receptive field changed to a dark patch. | | `Sn_stim_PSTH_offSub_lightRF` | `np.array` | (2001,) | PSTH for the offset of stimulus change where the stimilus on the unit's 'OFF' receptive field changed to a light patch. | | `Sn_stim_PSTH_offSub_bckgndRF` | `np.array` | (2001,) | PSTH for the offset of stimulus change where the stimilus everywhere except the unit's 'OFF' receptive field changed. | | `Sn_approx_onSub_RF_coords` | `np.array` | (4,) | Approximate coordinates of the receptive field for the 'ON' subunit. | | `Sn_approx_offSub_RF_coords` | `np.array` | (4,) | Approximate coordinates of the receptive field for the 'OFF' subunit. | | `Sn_stimT_all_shared` | `np.array` | (N,) | Times of stimulus changes where the stimulus changed everywhere. | | `Sn_stimT_unit_offSub_allT` | `np.array` | (N,) | Times of stimulus changes where the stimulus changed on the unit's 'OFF' receptive field. | | `Sn_stimT_unit_offSub_darkT` | `np.array` | (N,) | Times of stimulus changes where the stimulus changed on the unit's 'OFF' receptive field to a dark patch. | | `Sn_stimT_unit_offSub_lightT` | `np.array` | (N,) | Times of stimulus changes where the stimulus changed on the unit's 'OFF' receptive field to a light patch. | | `Sn_stimT_unit_offSub_bckgndT` | `np.array` | (N,) | Times of stimulus changes where the stimulus changed everywhere except the unit's 'OFF' receptive field. | | `Sn_stimT_unit_onSub_allT` | `np.array` | (N,) | Times of stimulus changes where the stimulus changed on the unit's 'ON' receptive field. | | `Sn_stimT_unit_onSub_darkT` | `np.array` | (N,) | Times of stimulus changes where the stimulus changed on the unit's 'ON' receptive field to a dark patch. | | `Sn_stimT_unit_onSub_lightT` | `np.array` | (N,) | Times of stimulus changes where the stimulus changed on the unit's 'ON' receptive field to a light patch. | | `Sn_stimT_unit_onSub_bckgndT` | `np.array` | (N,) | Times of stimulus changes where the stimulus changed everywhere except the unit's 'ON' receptive field. | | `Sn_recalc_stim_psth` | `np.array` | (2001,) | PSTH for stimulus change. Only exists for the hffl dataset. | | `Sn_norm_psth` | `np.array` | (2001,) | Normalized PSTH. Only exists for the hffl dataset. | | `raw_mod_for_Sn` | `float` | () | Raw modulation index for the stimulus. Only exists for the hffl dataset. | | `norm_mod_for_Sn` | `float` | () | Normalized modulation index for the stimulus. Only exists for the hffl dataset. | | `Sncluster_ind` | `int` | () | Cluster index for the stimulus. Only exists for the hffl dataset. | | `Sn_cluster` | `str` | () | Cluster for the stimulus. Only exists for the hffl dataset. | #### White noise stimulus | Name | Type | Shape | Description | | ---- | ---- | ----- | ----------- | | `Wn_active_fr` | `float64` | () | Average firing rate during active periods. | | `Wn_ballspeed` | `np.array` | (`len(ballT)`,) | Treadmill speed, in units of cm/sec. | | `Wn_ballspeed_modind` | `float64` | () | Modulation index for ball speed. | | `Wn_ballspeed_tuning` | `np.array` | (11,) | Ball speed tuning curve. | | `Wn_ballspeed_tuning_bins` | `np.array` | (11,) | Ball speed tuning curve bins. Each of these is the bin center (not the edge). | | `Wn_ballspeed_tuning_err` | `np.array` | (11,) | Ball speed tuning curve error at each bin. | | `Wn_contrast` | `np.array` | (`len(worldT)`,) | Contrast of the stimulus at each time point, aquired through the worldcam. | | `Wn_contrast_modind` | `float64` | () | Modulation index for contrast. | | `Wn_contrast_tuning` | `np.array` | (11,) | Contrast tuning curve. | | `Wn_contrast_tuning_bins` | `np.array` | (11,) | Contrast tuning curve bins. Each of these is the bin center (not the edge.) | | `Wn_contrast_tuning_err` | `np.array` | (11,) | Contrast tuning curve error at each bin. | | `Wn_dEye` | `np.array` | (`len(eyeT)-1`,) | Eye movement velocity in units of deg/sec. | | `Wn_dEye_dpf` | `np.array` | (`len(eyeT)-1`,) | Eye movement velocity in units of deg/frame. | | `Wn_depth_from_layer5` | `float` | () | Depth of the cell from layer 5 in um. | | `Wn_evoked_rate` | `float64` | () | Evoked firing rate during the stimulus. | | `Wn_eyeT` | `np.array` | (`len(eyeT)`,) | Eye camera timestamps relative to `Wn_t0`. Values from before the first ephys spike are negative. | | `Wn_inactive_fr` | `float64` | () | Average firing rate during inactive periods. | | `Wn_layer5cent_from_lfp` | `float` | () | Distance in um between center of cortical layer 5 and the neuron, calculated from LFP power. | | `Wn_leftsacc_avg` | `np.array` | (2001,) | Average PSTH for leftward saccades. | | `Wn_lfp_power` | `list` | (n_shanks,) | LFP power for each unit on shank. | | `Wn_max_contrast_rate` | `float64` | () | Maximum firing rate during the highest contrast. | | `Wn_n_spikes` | `float` | () | Number of spikes during all stimuli combined. | | `Wn_phi` | `np.array` | (`len(eyeT)`,) | Phi position of the head, in units of degrees. | | `Wn_phi_modind` | `float64` | () | Modulation index for phi. | | `Wn_phi_tuning` | `np.array` | (9,) | Phi tuning curve. | | `Wn_phi_tuning_bins` | `np.array` | (9,) | Phi tuning curve bins. Each of these is the bin center (not the edge). | | `Wn_phi_tuning_err` | `np.array` | (9,) | Phi tuning curve error at each bin. | | `Wn_pupilradius_modind` | `float64` | () | Modulation index for pupil radius. | | `Wn_pupilradius_tuning` | `np.array` | (9,) | Pupil radius tuning curve. | | `Wn_pupilradius_tuning_bins` | `np.array` | (9,) | Pupil radius tuning curve bins. Each of these is the bin center (not the edge). | | `Wn_pupilradius_tuning_err` | `np.array` | (9,) | Pupil radius tuning curve error at each bin. | | `Wn_rate` | `np.array` | (N,) | Spike rate for all stimuli interpolated to `modelT`. | | `Wn_rf_on_cent1` | `list` | (2,) or (4,) | Center of receptive field for each shank. | | `Wn_rightsacc_avg` | `np.array` | (2001,) | Average PSTH for rightward saccades. | | `Wn_spikeT` | `np.array` | (N,) | Spike times, in units of seconds. | | `Wn_spikeTraw` | `list` | (N,) | Spike times, in units of seconds. This is without correcting the drift and offset in data aquisition. | | `Wn_spike_triggered_average` | `np.array` | (60, 80) | Spike triggered average. | | `Wn_spike_triggered_variance` | `np.array` | (60, 80) | Spike triggered variance. | | `Wn_spont_rate` | `float64` | () | Spontaneous firing rate. | | `Wn_theta` | `np.array` | (`len(eyeT)`,) | Theta position of the head, in units of degrees. | | `Wn_theta_tuning` | `np.array` | (9,) | Theta tuning curve. | | `Wn_theta_tuning_bins` | `np.array` | (9,) | Theta tuning curve bins. Each of these is the bin center (not the edge). | | `Wn_theta_tuning_err` | `np.array` | (9,) | Theta tuning curve error at each bin. | #### Freely moving dark condition | Name | Type | Shape | Description | | ---- | ---- | ----- | ----------- | | `FmDk_n_spikes` | `np.ndarray` | (N,) | Number of spikes fired. | | `FmDk_spikeT` | `np.array` | (N,) | Spike times, in units of seconds. | | `FmDk_spikeTraw` | `np.array` | (N,) | Spike times, in units of seconds. This is without correcting the drift and offset in data aquisition. | | `FmDk_rate` | `np.array` | (N,) | Spike rate for all stimuli interpolated to `modelT`. | | `FmDk_contrast_tuning_bins` | `np.array` | (11,) | Contrast tuning curve bins. Each of these is the bin center (not the edge.) | | `FmDk_contrast_tuning` | `np.array` | (11,) | Contrast tuning curve. | | `FmDk_contrast_tuning_err` | `np.array` | (11,) | Contrast tuning curve error at each bin. | | `FmDk_spike_triggered_average` | `np.array` | (60, 80) | Spike triggered average. | | `FmDk_spike_triggered_variance` | `np.array` | (60, 80) | Spike triggered variance. | | `FmDk_pupilradius_tuning_bins` | `np.array` | (9,) | Pupil radius tuning curve bins. Each of these is the bin center (not the edge). | | `FmDk_pupilradius_tuning` | `np.array` | (9,) | Pupil radius tuning curve. | | `FmDk_pupilradius_tuning_err` | `np.array` | (9,) | Pupil radius tuning curve error at each bin. | | `FmDk_theta_tuning_bins` | `np.array` | (9,) | Theta tuning curve bins. Each of these is the bin center (not the edge). | | `FmDk_theta_tuning` | `np.array` | (9,) | Theta tuning curve. | | `FmDk_theta_tuning_err` | `np.array` | (9,) | Theta tuning curve error at each bin. | | `FmDk_phi_tuning_bins` | `np.array` | (9,) | Phi tuning curve bins. Each of these is the bin center (not the edge). | | `FmDk_phi_tuning` | `np.array` | (9,) | Phi tuning curve. | | `FmDk_phi_tuning_err` | `np.array` | (9,) | Phi tuning curve error at each bin. | | `FmDk_gyroz_tuning_bins` | `np.array` | (11,) | Gyro z tuning curve bins. Each of these is the bin center (not the edge). | | `FmDk_gyroz_tuning` | `np.array` | (11,) | Gyro z tuning curve. | | `FmDk_gyroz_tuning_err` | `np.array` | (11,) | Gyro z tuning curve error at each bin. | | `FmDk_gyrox_tuning_bins` | `np.array` | (11,) | Gyro x tuning curve bins. Each of these is the bin center (not the edge). | | `FmDk_gyrox_tuning` | `np.array` | (11,) | Gyro x tuning curve. | | `FmDk_gyrox_tuning_err` | `np.array` | (11,) | Gyro x tuning curve error at each bin. | | `FmDk_gyroy_tuning_bins` | `np.array` | (11,) | Gyro y tuning curve bins. Each of these is the bin center (not the edge). | | `FmDk_gyroy_tuning` | `np.array` | (11,) | Gyro y tuning curve. | | `FmDk_gyroy_tuning_err` | `np.array` | (11,) | Gyro y tuning curve error at each bin. | | `FmDk_imuT` | `np.array` | (N,) | IMU timestamps relative to `FmDk_t0`. Values from before the first ephys spike are negative. | | `FmDk_gyro_x` | `np.array` | (`len(imuT)`,) | Gyro x position. | | `FmDk_gyro_y` | `np.array` | (`len(imuT)`,) | Gyro y position. | | `FmDk_gyro_z` | `np.array` | (`len(imuT)`,) | Gyro z position. | | `FmDk_dHead` | `np.array` | (`len(imuT)`,) | Change in head position. | | `FmDk_eyeT` | `np.array` | (N,) | Eye camera timestamps relative to `FmDk_t0`. Values from before the first ephys spike are negative. | | `FmDk_dEye_dpf` | `np.array` | (`len(eyeT)-1`,) | Eye movement velocity in units of deg/frame. | | `FmDk_theta` | `np.array` | (`len(eyeT)`,) | Theta position of the eye, in units of degrees. | | `FmDk_phi` | `np.array` | (`len(eyeT)`,) | Phi position of the eye, in units of degrees. | | `FmDk_dGaze` | `np.array` | (`len(eyeT)-1`,) | Change in gaze position. | | `FmDk_roll_tuning_bins` | `np.array` | (11,) | Roll tuning curve bins. Each of these is the bin center (not the edge). | | `FmDk_roll_tuning` | `np.array` | (11,) | Roll tuning curve. | | `FmDk_roll_tuning_err` | `np.array` | (11,) | Roll tuning curve error at each bin. | | `FmDk_pitch_tuning_bins` | `np.array` | (11,) | Pitch tuning curve bins. Each of these is the bin center (not the edge). | | `FmDk_pitch_tuning` | `np.array` | (11,) | Pitch tuning curve. | | `FmDk_pitch_tuning_err` | `np.array` | (11,) | Pitch tuning curve error at each bin. | | `FmDk_roll` | `np.array` | (`len(eyeT)`,) | Roll position of the eye, in units of degrees. | | `FmDk_pitch` | `np.array` | (`len(eyeT)`,) | Pitch position of the eye, in units of degrees. | | `FmDk_gyroz_modind` | `float64` | () | Modulation index for gyro z. | | `FmDk_gyrox_modind` | `float64` | () | Modulation index for gyro x. | | `FmDk_gyroy_modind` | `float64` | () | Modulation index for gyro y. | | `FmDk_pupilradius_modind` | `float64` | () | Modulation index for pupil radius. | | `FmDk_theta_modind` | `float64` | () | Modulation index for theta. | | `FmDk_phi_modind` | `float64` | () | Modulation index for phi. | | `FmDk_roll_modind` | `float64` | () | Modulation index for roll. | | `FmDk_pitch_modind` | `float64` | () | Modulation index for pitch. | | `FmDk_gazeshift_left_saccPSTH` | `np.array` | (2001,) | PSTH for leftward saccades. | | `FmDk_gazeshift_left_saccTimes` | `np.array` | (N,) | Times for leftward saccades. | | `FmDk_gazeshift_right_saccPSTH` | `np.array` | (2001,) | PSTH for rightward saccades. | | `FmDk_gazeshift_right_saccTimes` | `np.array` | (N,) | Times for rightward saccades. | | `FmDk_compensatory_left_saccPSTH` | `np.array` | (2001,) | PSTH for leftward saccades. | | `FmDk_compensatory_left_saccTimes` | `np.array` | (N,) | Times for leftward saccades. | | `FmDk_compensatory_right_saccPSTH` | `np.array` | (2001,) | PSTH for rightward saccades. | | `FmDk_compensatory_right_saccTimes` | `np.array` | (N,) | Times for rightward saccades. | | `pref_gazeshift_psth_FmDk` | `np.array` | (2001,) | PSTH for preferred direction gaze shifts. | | `pref_comp_psth_FmDk` | `np.array` | (2001,) | PSTH for preferred direction compensatory saccades. | | `nonpref_gazeshift_psth_FmDk` | `np.array` | (2001,) | PSTH for non-preferred direction gaze shifts. | | `nonpref_comp_psth_FmDk` | `np.array` | (2001,) | PSTH for non-preferred direction compensatory saccades. | | `gaze_ltdk_maxcc` | `float64` | () | Maximum cross correlation between the freely moving gaze shift PSTH in the light versus dark. | | `FmDk_gazeshift_baseline` | `float64` | () | Baseline firing rate for gaze shifts. | | `FmDk_gazeshift_peakT` | `float64` | () | Time of peak firing rate for gaze shifts. | | `FmDk_gazeshift_troughT` | `float64` | () | Time of trough firing rate for gaze shifts. | | `gaze_sacc_rlMI` | `float64` | () | Right/left modulation index. | | `comp_sacc_rlMI` | `float64` | () | Right/left modulation index. | | `gaze_sacc_pnpMI` | `float64` | () | Preferred/non-preferred modulation index. | | `comp_sacc_pnpMI` | `float64` | () | Preferred/non-preferred modulation index. | | `FmDk_fr` | `float64` | () | Average firing rate. | | `FmLt_modelT` | `np.array` | () | Time points for locomotion activity. | | `FmDk_model_active` | `np.array` | () | Dark condition locomotion activity. | | `FmDk_active_fr` | `float64` | () | Average firing rate during locomotion. | | `FmDk_inactive_fr` | `float64` | () | Average firing rate during inactivity. | | `pref_dark_gazeshift_psth` | `np.array` | (2001,) | PSTH for preferred direction gaze shifts. | | `nonpref_dark_gazeshift_psth` | `np.array` | (2001,) | PSTH for non-preferred direction gaze shifts. | | `pref_dark_comp_psth` | `np.array` | (2001,) | PSTH for preferred direction compensatory saccades. | | `nonpref_dark_comp_psth` | `np.array` | (2001,) | PSTH for non-preferred direction compensatory saccades. | | `pref_dark_gazeshift_psth_raw` | `np.array` | (2001,) | PSTH for preferred direction gaze shifts. | | `nonpref_dark_gazeshift_psth_raw` | `np.array` | (2001,) | PSTH for non-preferred direction gaze shifts. | | `pref_dark_comp_psth_raw` | `np.array` | (2001,) | PSTH for preferred direction compensatory saccades. | | `nonpref_dark_comp_psth_raw` | `np.array` | (2001,) | PSTH for non-preferred direction compensatory saccades. | | `FmDk_gazeshift_med_baseline` | `float64` | () | Median baseline firing rate for gaze shifts. | | `FmDk_gazeshift_peak_val` | `float64` | () | Peak firing rate for gaze shifts. | | `norm_mod_at_pref_peak_dark` | `float64` | () | Normalized modulation at preferred peak. | | `raw_mod_at_pref_peak_dark` | `float64` | () | Raw modulation at preferred peak. | | `dark_peak_val` | `float64` | () | Peak firing rate of prefered direction of PSTH in the dark. | | `dark_peakT` | `float64` | () | Time of peak firing rate of prefered direction of PSTH in the dark. | | `dark_responsive` | `bool` | () | Whether or not the cell was responsive in dark condition. | #### Sparse noise with Inter-Stimulus Interval (ISI) Sparse noise presented with an inter-stimulus interval. | Name | Type | Shape | Description | | ---- | ---- | ----- | ----------- | | `hasSnI` | `bool` | () | Whether or not the unit has data for sparse noise presented with an ISI. | | `SnI_Amplitude` | `float64` | () | Spike amplitude. | | `SnI_ContamPct` | `float64` | () | Contamination percentage. | | `SnI_KSLabel` | `str` | () | KS label. | | `SnI_amp` | `float64` | () | Spike amplitude. | | `SnI_ch` | `int` | () | Channel. | | `SnI_depth` | `float64` | () | Depth. | | `SnI_fr` | `float64` | () | Average firing rate. | | `SnI_group` | `int` | () | Group. | | `SnI_n_spikes` | `float64` | () | Number of spikes. | | `SnI_sh` | `int` | () | Shank. | | `SnI_waveform` | `np.array` | (40,) | Spike waveform. | | `SnI_spikeT` | `np.array` | (N,) | Spike times, in units of seconds. | | `SnI_t0` | `float64` | () | Time of first spike. | | `SnI_spikeTraw` | `np.array` | (N,) | Spike times, in units of seconds. This is without correcting the drift and offset in data aquisition. | | `SnI_rate` | `np.array` | (N,) | Spike rate for all stimuli interpolated to `modelT`. | | `SnI_contrast` | `np.array` | (`len(worldT)`,) | Contrast of the stimulus at each time point, aquired through the worldcam. | | `SnI_contrast_tuning_bins` | `np.array` | (11,) | Contrast tuning curve bins. Each of these is the bin center (not the edge.) | | `SnI_contrast_tuning` | `np.array` | (11,) | Contrast tuning curve. | | `SnI_contrast_tuning_err` | `np.array` | (11,) | Contrast tuning curve error at each bin. | | `SnI_spike_triggered_average` | `np.array` | (60, 80) | Spike triggered average. | | `SnI_spike_triggered_variance` | `np.array` | (60, 80) | Spike triggered variance. | | `SnI_saccade_rightT` | `np.array` | (N,) | Times for rightward saccades. | | `SnI_saccade_leftT` | `np.array` | (N,) | Times for leftward saccades. | | `SnI_saccade_rightPSTH` | `np.array` | (2001,) | PSTH for rightward saccades. | | `SnI_saccade_leftPSTH` | `np.array` | (2001,) | PSTH for leftward saccades. | | `SnI_pupilradius_tuning_bins` | `np.array` | (9,) | Pupil radius tuning curve bins. Each of these is the bin center (not the edge). | | `SnI_pupilradius_tuning` | `np.array` | (9,) | Pupil radius tuning curve. | | `SnI_pupilradius_tuning_err` | `np.array` | (9,) | Pupil radius tuning curve error at each bin. | | `SnI_theta_tuning_bins` | `np.array` | (9,) | Theta tuning curve bins. Each of these is the bin center (not the edge). | | `SnI_theta_tuning` | `np.array` | (9,) | Theta tuning curve. | | `SnI_theta_tuning_err` | `np.array` | (9,) | Theta tuning curve error at each bin. | | `SnI_phi_tuning_bins` | `np.array` | (9,) | Phi tuning curve bins. Each of these is the bin center (not the edge). | | `SnI_phi_tuning` | `np.array` | (9,) | Phi tuning curve. | | `SnI_phi_tuning_err` | `np.array` | (9,) | Phi tuning curve error at each bin. | | `SnI_eyeT` | `np.array` | (`len(eyeT)`,) | Eye camera timestamps relative to `SnI_t0`. Values from before the first ephys spike are negative. | | `SnI_dEye_dpf` | `np.array` | (`len(eyeT)-1`,) | Eye movement velocity in units of deg/frame. | | `SnI_dEye_dps` | `np.array` | (`len(eyeT)-1`,) | Eye movement velocity in units of deg/sec. | | `SnI_theta` | `np.array` | (`len(eyeT)`,) | Theta position of the head, in units of degrees. | | `SnI_phi` | `np.array` | (`len(eyeT)`,) | Phi position of the head, in units of degrees. | | `SnI_ballspeed` | `np.array` | (`len(ballT)`,) | Treadmill speed, in units of cm/sec. | | `SnI_ballspeed_tuning_bins` | `np.array` | (11,) | Ball speed tuning curve bins. Each of these is the bin center (not the edge). | | `SnI_ballspeed_tuning` | `np.array` | (11,) | Ball speed tuning curve. | | `SnI_ballspeed_tuning_err` | `np.array` | (11,) | Ball speed tuning curve error at each bin. | | `SnI_worldT` | `np.array` | (`len(worldT)`,) | World camera timestamps relative to `SnI_t0`. Values from before the first ephys spike are negative. | | `SnI_stim_PSTH_onSub_all` | `np.array` | (2001,) | PSTH for the onset of stimulus change where the stimilus on the unit's 'ON' receptive field changed. | | `SnI_stim_PSTH_onSub_darkRF` | `np.array` | (2001,) | PSTH for the onset of stimulus change where the stimilus on the unit's 'ON' receptive field changed to a dark patch. | | `SnI_stim_PSTH_onSub_lightRF` | `np.array` | (2001,) | PSTH for the onset of stimulus change where the stimilus on the unit's 'ON' receptive field changed to a light patch. | | `SnI_stim_PSTH_onSub_bckgndRF` | `np.array` | (2001,) | PSTH for the onset of stimulus change where the stimilus everywhere except the unit's 'ON' receptive field changed. | | `SnI_stim_PSTH_offSub_all` | `np.array` | (2001,) | PSTH for the offset of stimulus change where the stimilus on the unit's 'OFF' receptive field changed. | | `SnI_stim_PSTH_offSub_darkRF` | `np.array` | (2001,) | PSTH for the offset of stimulus change where the stimilus on the unit's 'OFF' receptive field changed to a dark patch. | | `SnI_stim_PSTH_offSub_lightRF` | `np.array` | (2001,) | PSTH for the offset of stimulus change where the stimilus on the unit's 'OFF' receptive field changed to a light patch. | | `SnI_stim_PSTH_offSub_bckgndRF` | `np.array` | (2001,) | PSTH for the offset of stimulus change where the stimilus everywhere except the unit's 'OFF' receptive field changed. | | `SnI_approx_onSub_RF_coords` | `np.array` | (4,) | Approximate coordinates of the receptive field for the 'ON' subunit. | | `SnI_approx_offSub_RF_coords` | `np.array` | (4,) | Approximate coordinates of the receptive field for the 'OFF' subunit. | | `SnI_stimT_all_shared` | `np.array` | (N,) | Times of stimulus changes where the stimulus changed everywhere. | | `SnI_stimT_unit_offSub_allT` | `np.array` | (N,) | Times of stimulus changes where the stimulus changed on the unit's 'OFF' receptive field. | | `SnI_stimT_unit_offSub_darkT` | `np.array` | (N,) | Times of stimulus changes where the stimulus changed on the unit's 'OFF' receptive field to a dark patch. | | `SnI_stimT_unit_offSub_lightT` | `np.array` | (N,) | Times of stimulus changes where the stimulus changed on the unit's 'OFF' receptive field to a light patch. | | `SnI_stimT_unit_offSub_bckgndT` | `np.array` | (N,) | Times of stimulus changes where the stimulus changed everywhere except the unit's 'OFF' receptive field. | | `SnI_stimT_unit_onSub_allT` | `np.array` | (N,) | Times of stimulus changes where the stimulus changed on the unit's 'ON' receptive field. | | `SnI_stimT_unit_onSub_darkT` | `np.array` | (N,) | Times of stimulus changes where the stimulus changed on the unit's 'ON' receptive field to a dark patch. | | `SnI_stimT_unit_onSub_lightT` | `np.array` | (N,) | Times of stimulus changes where the stimulus changed on the unit's 'ON' receptive field to a light patch. | | `SnI_stimT_unit_onSub_bckgndT` | `np.array` | (N,) | Times of stimulus changes where the stimulus changed everywhere except the unit's 'ON' receptive field. | | `SnI_recalc_stim_psth` | `np.array` | (2001,) | PSTH for all background / full-field stimulus changes. | | `SnI_norm_psth` | `np.array` | (2001,) | PSTH for all background / full-field stimulus changes, normalized. | | `raw_mod_for_SnI` | `float` | () | PSTH modulation index measured from the raw PSTH. | | `norm_mod_for_SnI` | `float` | () | PSTH modulation index measured from the normalized PSTH. | | `SnI_responsive` | `bool` | () | Whether or not the unit was responsive to the sparse noise with ISI stimulus. | | `SnIcluster_ind` | `int` | () | Cluster index for the sparse noise with ISI stimulus. | | `SnI_cluster` | `str` | () | Cluster label for the sparse noise with ISI stimulus. | #### Sparse noise with random stimulus duration | Name | Type | Shape | Description | | ---- | ---- | ----- | ----------- | | `hasSnR` | `bool` | () | Whether or not the unit has sparse noise with random stimulus duration. | | `SnR_Amplitude` | `float64` | () | Spike amplitude. | | `SnR_ContamPct` | `float64` | () | Contamination percentage. | | `SnR_KSLabel` | `str` | () | KS label. | | `SnR_amp` | `float64` | () | Spike amplitude. | | `SnR_ch` | `int` | () | Channel. | | `SnR_depth` | `float64` | () | Depth. | | `SnR_fr` | `float64` | () | Average firing rate. | | `SnR_group` | `int` | () | Group. | | `SnR_n_spikes` | `float64` | () | Total number of spikes. | | `SnR_sh` | `int` | () | Shank number. | | `SnR_waveform` | `np.array` | (40,) | Spike waveform. | | `SnR_spikeT` | `np.array` | (N,) | Spike times, in units of seconds. | | `SnR_t0` | `float64` | () | Time of first spike. | | `SnR_spikeTraw` | `np.array` | (N,) | Spike times, in units of seconds. This is without correcting the drift and offset in data aquisition. | | `SnR_rate` | `np.array` | (N,) | Spike rate for all stimuli interpolated to `modelT`. | | `SnR_contrast` | `np.array` | (`len(worldT)`,) | Contrast of the stimulus at each time point, aquired through the worldcam. | | `SnR_contrast_tuning_bins` | `np.array` | (11,) | Contrast tuning curve bins. Each of these is the bin center (not the edge.) | | `SnR_contrast_tuning` | `np.array` | (11,) | Contrast tuning curve. | | `SnR_contrast_tuning_err` | `np.array` | (11,) | Contrast tuning curve error at each bin. | | `SnR_spike_triggered_average` | `np.array` | (60, 80) | Spike triggered average. | | `SnR_spike_triggered_variance` | `np.array` | (60, 80) | Spike triggered variance. | | `SnR_saccade_rightT` | `np.array` | (N,) | Times for rightward saccades. | | `SnR_saccade_leftT` | `np.array` | (N,) | Times for leftward saccades. | | `SnR_saccade_rightPSTH` | `np.array` | (2001,) | PSTH for rightward saccades. | | `SnR_saccade_leftPSTH` | `np.array` | (2001,) | PSTH for leftward saccades. | | `SnR_pupilradius_tuning_bins` | `np.array` | (9,) | Pupil radius tuning curve bins. Each of these is the bin center (not the edge). | | `SnR_pupilradius_tuning` | `np.array` | (9,) | Pupil radius tuning curve. | | `SnR_pupilradius_tuning_err` | `np.array` | (9,) | Pupil radius tuning curve error at each bin. | | `SnR_theta_tuning_bins` | `np.array` | (9,) | Theta tuning curve bins. Each of these is the bin center (not the edge). | | `SnR_theta_tuning` | `np.array` | (9,) | Theta tuning curve. | | `SnR_theta_tuning_err` | `np.array` | (9,) | Theta tuning curve error at each bin. | | `SnR_phi_tuning_bins` | `np.array` | (9,) | Phi tuning curve bins. Each of these is the bin center (not the edge). | | `SnR_phi_tuning` | `np.array` | (9,) | Phi tuning curve. | | `SnR_phi_tuning_err` | `np.array` | (9,) | Phi tuning curve error at each bin. | | `SnR_eyeT` | `np.array` | (`len(eyeT)`,) | Eye camera timestamps relative to `SnR_t0`. Values from before the first ephys spike are negative. | | `SnR_dEye_dpf` | `np.array` | (`len(eyeT)-1`,) | Eye movement velocity in units of deg/frame. | | `SnR_dEye_dps` | `np.array` | (`len(eyeT)-1`,) | Eye movement velocity in units of deg/sec. | | `SnR_theta` | `np.array` | (`len(eyeT)`,) | Theta position of the head, in units of degrees. | | `SnR_phi` | `np.array` | (`len(eyeT)`,) | Phi position of the head, in units of degrees. | | `SnR_ballspeed` | `np.array` | (`len(ballT)`,) | Treadmill speed, in units of cm/sec. | | `SnR_ballspeed_tuning_bins` | `np.array` | (11,) | Ball speed tuning curve bins. Each of these is the bin center (not the edge). | | `SnR_ballspeed_tuning` | `np.array` | (11,) | Ball speed tuning curve. | | `SnR_ballspeed_tuning_err` | `np.array` | (11,) | Ball speed tuning curve error at each bin. | | `SnR_stim_PSTH_onSub_all` | `np.array` | (2001,) | PSTH for the onset of stimulus change where the stimilus on the unit's 'ON' receptive field changed. | | `SnR_stim_PSTH_onSub_darkRF` | `np.array` | (2001,) | PSTH for the onset of stimulus change where the stimilus on the unit's 'ON' receptive field changed to a dark patch. | | `SnR_stim_PSTH_onSub_lightRF` | `np.array` | (2001,) | PSTH for the onset of stimulus change where the stimilus on the unit's 'ON' receptive field changed to a light patch. | | `SnR_stim_PSTH_onSub_bckgndRF` | `np.array` | (2001,) | PSTH for the onset of stimulus change where the stimilus everywhere except the unit's 'ON' receptive field changed. | | `SnR_stim_PSTH_offSub_all` | `np.array` | (2001,) | PSTH for the offset of stimulus change where the stimilus on the unit's 'OFF' receptive field changed. | | `SnR_stim_PSTH_offSub_darkRF` | `np.array` | (2001,) | PSTH for the offset of stimulus change where the stimilus on the unit's 'OFF' receptive field changed to a dark patch. | | `SnR_stim_PSTH_offSub_lightRF` | `np.array` | (2001,) | PSTH for the offset of stimulus change where the stimilus on the unit's 'OFF' receptive field changed to a light patch. | | `SnR_stim_PSTH_offSub_bckgndRF` | `np.array` | (2001,) | PSTH for the offset of stimulus change where the stimilus everywhere except the unit's 'OFF' receptive field changed. | | `SnR_approx_onSub_RF_coords` | `np.array` | (4,) | Approximate coordinates of the receptive field for the 'ON' subunit. | | `SnR_approx_offSub_RF_coords` | `np.array` | (4,) | Approximate coordinates of the receptive field for the 'OFF' subunit. | | `SnR_stimT_all_shared` | `np.array` | (N,) | Times of stimulus changes where the stimulus changed everywhere. | | `SnR_stimT_unit_offSub_allT` | `np.array` | (N,) | Times of stimulus changes where the stimulus changed on the unit's 'OFF' receptive field. | | `SnR_stimT_unit_offSub_darkT` | `np.array` | (N,) | Times of stimulus changes where the stimulus changed on the unit's 'OFF' receptive field to a dark patch. | | `SnR_stimT_unit_offSub_lightT` | `np.array` | (N,) | Times of stimulus changes where the stimulus changed on the unit's 'OFF' receptive field to a light patch. | | `SnR_stimT_unit_offSub_bckgndT` | `np.array` | (N,) | Times of stimulus changes where the stimulus changed everywhere except the unit's 'OFF' receptive field. | | `SnR_stimT_unit_onSub_allT` | `np.array` | (N,) | Times of stimulus changes where the stimulus changed on the unit's 'ON' receptive field. | | `SnR_stimT_unit_onSub_darkT` | `np.array` | (N,) | Times of stimulus changes where the stimulus changed on the unit's 'ON' receptive field to a dark patch. | | `SnR_stimT_unit_onSub_lightT` | `np.array` | (N,) | Times of stimulus changes where the stimulus changed on the unit's 'ON' receptive field to a light patch. | | `SnR_stimT_unit_onSub_bckgndT` | `np.array` | (N,) | Times of stimulus changes where the stimulus changed everywhere except the unit's 'ON' receptive field. | | `SnR_norm_psth` | `np.array` | (2001,) | PSTH for all background / full-field stimulus changes, normalized. | ### Marmoset data | Name | Type | Shape | Description | | ---- | ---- | ----- | ----------- | | `PSTH` | `np.array` | (2001,) | PSTH aligned to saccade onset. | | `normPSTH` | `np.array` | (2001,) | Normalized PSTH. | | `sf_tuning` | `np.array` | (N,) | Spatial frequency tuning curve. | | `tf_tuning` | `np.array` | (N,) | Temporal frequency tuning curve. | | `ori_tuning` | `np.array` | (N,) | Orientation tuning curve. | | `spikeT` | `np.array` | (N,) | Spike times, in units of seconds. | | `session` | `float` | () | NaNs | | `gazecluster` | `str` | () | Gaze shift response cluster. | | `gazecluster_ind` | `int` | () | NaNs | | `animal` | `int` | () | Animal number. | | `sf_pref` | `float` | () | Spatial frequency preference. | | `tf_pref` | `float` | () | Temporal frequency preference. | | `gratings_responsive` | `bool` | () | Whether or not the cell was responsive to gratings. | | `peakT` | `float` | () | Peak latency following | | `baseline_fr` | `float` | () | Baseline firing rate. | | `saccade_responsive` | `bool` | () | Whether or not the cell was responsive to saccades. | ## Code/Software All original Python code is avaliable on GitHub. Acquisition and preprocessing code: [FreelyMovingEphys](https://github.com/nielllab/FreelyMovingEphys). Analysis and figure code: [freely-moving-saccades](https://github.com/nielllab/freely-moving-saccades). These repositories can be installed and imported as the packages `fmEphys` and `saccadeAnalysis`, respectively (see repositiory READMEs for installation instructions). The hdf files can be read in as: ``` import fmEphys as fme # Read the file in. hffm = fme.read_group_hdf('/.../hffm.h5') # Index into the eye camera timestamps for unit zero. The output will be an array. hffm.iloc[0,'FmLt_eyeT'] ```