allensdk.brain_observatory.ecephys.stimulus_analysis.static_gratings module

class allensdk.brain_observatory.ecephys.stimulus_analysis.static_gratings.StaticGratings(ecephys_session, col_ori='orientation', col_sf='spatial_frequency', col_phase='phase', trial_duration=0.25, **kwargs)

Bases: allensdk.brain_observatory.ecephys.stimulus_analysis.stimulus_analysis.StimulusAnalysis

A class for computing single-unit metrics from the static gratings stimulus of an ecephys session NWB file.

To use, pass in a EcephysSession object::

session = EcephysSession.from_nwb_path(‘/path/to/my.nwb’) sg_analysis = StaticGratings(session)

or, alternatively, pass in the file path::

sg_analysis = StaticGratings(‘/path/to/my.nwb’)

You can also pass in a unit filter dictionary which will only select units with certain properties. For example to get only those units which are on probe C and found in the VISp area:

sg_analysis = StaticGratings(session, filter={'location': 'probeC', 'ecephys_structure_acronym': 'VISp'})

To get a table of the individual unit metrics ranked by unit ID::

metrics_table_df = sg_analysis.metrics()

METRICS_COLUMNS

classmethod known_stimulus_keys()

Used for discovering the correct stimulus_name key for a given StimulusAnalysis subclass (when stimulus_key is not explicity set). Should return a list of “stimulus_name” strings.

make_fan_plot(self, unit_id)

Make a 2P-style Fan Plot based on presentationwise spike counts

metrics

Returns a pandas DataFrame of the stimulus response metrics for each unit.

name

Return the stimulus name.

null_condition

Stimulus condition ID for null (blank) stimulus

number_ori

Number of grating orientation conditions

number_phase

Number of grating phase conditions

number_sf

Number of grating orientation conditions

orivals

Array of grating orientation conditions

phasevals

Array of grating phase conditions

plot_raster(self, stimulus_condition_id, unit_id)

Plot raster for one condition and one unit

plot_response_summary(self, unit_id, bar_thickness=0.25)

Plot the spike counts across conditions

sfvals

Array of grating spatial frequency conditions

allensdk.brain_observatory.ecephys.stimulus_analysis.static_gratings.exp_function(x, a, b, c)

allensdk.brain_observatory.ecephys.stimulus_analysis.static_gratings.fit_sf_tuning(sf_tuning_responses, sf_values, pref_sf_index)

Performs gaussian or exponential fit on the spatial frequency tuning curve at preferred orientation/phase for a given cell.

Parameters:

• sf_tuning_responses – An array of len N, with each value the (averaged) response of a cell at a given spatial freq. stimulus.
• sf_values – An array of len N, with each value the spatial freq. of the stimulus (corresponding to sf_tuning_response).
• pref_sf_index – The pre-determined prefered spatial frequency (sf_values index) of the cell.

Returns:

index for the preferred sf from the curve fit, prefered sf from the curve fit, low cutoff sf from the curve fit, high cutoff sf from the curve fit

allensdk.brain_observatory.ecephys.stimulus_analysis.static_gratings.gauss_function(x, a, x0, sigma)

allensdk.brain_observatory.ecephys.stimulus_analysis.static_gratings.get_sfdi(sf_tuning_responses, mean_sweeps_trials, bias=5)

Computes spatial frequency discrimination index for cell

Parameters:

• sf_tuning_responses – sf_tuning_responses: An array of len N, with each value the (averaged) response of a cell at a given spatial freq. stimulus.
• mean_sweeps_trials – The set of events (spikes) across all trials of varying
• bias –

Returns:

The sfdi value (float)