brainbox.task.passive

Functions dealing with passive task

Functions

get_on_off_times_and_positions

Prepares passive receptive field mapping into format for analysis :param rf_map: :type rf_map: output from brainbox.io.one.load_passive_rfmap

get_rf_map_over_depth

Compute receptive field map for each stimulus onset binned across depth :param rf_map_times: :param rf_map_pos: :param rf_stim_frames: :param spike_times: :type spike_times: array of spike times :param spike_depths: :type spike_depths: array of spike depths along probe :param t_bin: :type t_bin: bin size along time dimension :param d_bin: :type d_bin: bin size along depth dimension :param pre_stim: :type pre_stim: time period before rf map stim onset to epoch around :param post_stim: :type post_stim: time period after rf map onset to epoch around :param y_lim: :type y_lim: values to limit to in depth direction :param x_lim: :type x_lim: values to limit in time direction

get_stim_aligned_activity

param stim_events

get_svd_map

Perform SVD on the spatiotemporal rf_map and return the first spatial components :param rf_map:

get_on_off_times_and_positions(rf_map)[source]

Prepares passive receptive field mapping into format for analysis :param rf_map: :type rf_map: output from brainbox.io.one.load_passive_rfmap

Returns

  • rf_map_times (time of each receptive field map frame np.array(len(stim_frames))

  • rf_map_pos (unique position of each pixel on scree np.array(len(x_pos), len(y_pos)))

  • rf_stim_frames (for each pixel on screen stores array of stimulus frames where stim onset)

  • occured. For both white squares ‘on’ and black squares ‘off’

get_rf_map_over_depth(rf_map_times, rf_map_pos, rf_stim_frames, spike_times, spike_depths, t_bin=0.01, d_bin=80, pre_stim=0.05, post_stim=1.5, y_lim=[0, 3840], x_lim=None)[source]

Compute receptive field map for each stimulus onset binned across depth :param rf_map_times: :param rf_map_pos: :param rf_stim_frames: :param spike_times: :type spike_times: array of spike times :param spike_depths: :type spike_depths: array of spike depths along probe :param t_bin: :type t_bin: bin size along time dimension :param d_bin: :type d_bin: bin size along depth dimension :param pre_stim: :type pre_stim: time period before rf map stim onset to epoch around :param post_stim: :type post_stim: time period after rf map onset to epoch around :param y_lim: :type y_lim: values to limit to in depth direction :param x_lim: :type x_lim: values to limit in time direction

Returns

  • rfmap (receptive field map for ‘on’ ‘off’ stimuli.)

  • Each rfmap has shape (depths, x_pos, y_pos, epoch_window)

  • depths (depths between which receptive field map has been computed)

get_svd_map(rf_map)[source]

Perform SVD on the spatiotemporal rf_map and return the first spatial components :param rf_map:

Returns

  • rf_svd (First spatial component of rf map for ‘on’ ‘off’ stimuli.)

  • Each dict has shape (depths, x_pos, y_pos)

get_stim_aligned_activity(stim_events, spike_times, spike_depths, z_score_flag=True, d_bin=20, t_bin=0.01, pre_stim=0.4, post_stim=1, base_stim=1, y_lim=[0, 3840], x_lim=None)[source]
Parameters
  • stim_events (dict of different stim events. Each key contains time of stimulus onset) –

  • spike_times (array of spike times) –

  • spike_depths (array of spike depths along probe) –

  • z_score_flag (whether to return values as z_score of firing rate) –

  • T_BIN (bin size along time dimension) –

  • D_BIN (bin size along depth dimension) –

  • pre_stim (time period before rf map stim onset to epoch around) –

  • post_stim (time period after rf map onset to epoch around) –

  • base_stim (time period before rf map stim to use as baseline for z_score correction) –

  • y_lim (values to limit to in depth direction) –

  • x_lim (values to limit in time direction) –

Returns

  • stim_activity (stimulus aligned activity for each stimulus type, returned as z_score of firing)

  • rate