allensdk.brain_observatory.behavior.behavior_ophys_session module

class allensdk.brain_observatory.behavior.behavior_ophys_session.BehaviorOphysSession(api=None)

Bases: object

Represents data from a single Visual Behavior Ophys imaging session. Can be initialized with an api that fetches data, or by using class methods from_lims and from_nwb_path.

average_projection

2D image of the microscope field of view, averaged across the experiment :rtype: pandas.DataFrame

cache_clear(self) → None

Convenience method to clear the api cache, if applicable.

cell_specimen_table

Cell roi information organized into a dataframe; index is the cell roi ids. :rtype: pandas.DataFrame

corrected_fluorescence_traces

The motion-corrected fluorescence traces organized into a dataframe; index is the cell roi ids. :rtype: pandas.DataFrame

deserialize_image(self, sitk_image)

Convert SimpleITK image returned by the api to an Image class:

Args:

sitk_image (SimpleITK image): image object returned by the api

Returns

img (allensdk.brain_observatory.behavior.image_api.Image)

dff_traces

Traces of dff organized into a dataframe; index is the cell roi ids. :rtype: pandas.DataFrame

classmethod from_lims(ophys_experiment_id: int) → 'BehaviorOphysSession'

classmethod from_nwb_path(nwb_path: str, **api_kwargs: Any) → 'BehaviorOphysSession'

get_average_projection(self)

Returns an image whose values are the average obtained values at each pixel of the ophys movie over time.

Returns:

allensdk.brain_observatory.behavior.image_api.Image:

array-like interface to max projection image data and metadata

get_cell_specimen_ids(self)

get_cell_specimen_indices(self, cell_specimen_ids)

get_dff_traces(self, cell_specimen_ids=None)

get_max_projection(self)

Returns an image whose values are the maximum obtained values at each pixel of the ophys movie over time.

Returns:

allensdk.brain_observatory.behavior.image_api.Image:

array-like interface to max projection image data and metadata

get_performance_metrics(self, engaged_trial_reward_rate_threshold=2)

get_reward_rate(self)

get_roi_masks(self, cell_specimen_ids=None)

Obtains boolean masks indicating the location of one or more cell’s ROIs in this session.

Parameters:

cell_specimen_ids : array-like of int, optional

ROI masks for these cell specimens will be returned. The default behavior is to return masks for all cell specimens.

Returns:

result : xr.DataArray

dimensions are:

• cell_specimen_id : which cell’s roi is described by this mask?
• row : index within the underlying image
• column : index within the image

values are 1 where an ROI was present, otherwise 0.

get_rolling_performance_df(self)

get_segmentation_mask_image(self)

Returns an image with value 1 if the pixel was included in an ROI, and 0 otherwise

Returns:

allensdk.brain_observatory.behavior.image_api.Image:

array-like interface to segmentation_mask image data and metadata

licks

A dataframe containing lick timestamps. :rtype: pandas.DataFrame

max_projection

2D max projection image. :rtype: allensdk.brain_observatory.behavior.image_api.Image

metadata

Dictionary of session-specific metadata. :rtype: dict

motion_correction

A dataframe containing trace data used during motion correction computation :rtype: pandas.DataFrame

ophys_experiment_id

Unique identifier for this experimental session. :rtype: int

ophys_timestamps

Timestamps associated with frames captured by the microscope :rtype: numpy.ndarray

rewards

A dataframe containing timestamps of delivered rewards. :rtype: pandas.DataFrame

running_data_df

Dataframe containing various signals used to compute running speed :rtype: pandas.DataFrame

running_speed

Running speed of mouse. NamedTuple with two fields

timestamps : numpy.ndarray

Timestamps of running speed data samples

values : np.ndarray

Running speed of the experimental subject (in cm / s).

Return type:allensdk.brain_observatory.running_speed.RunningSpeed

segmentation_mask_image

An image with pixel value 1 if that pixel was included in an ROI, and 0 otherwise :rtype: allensdk.brain_observatory.behavior.image_api.Image

stimulus_presentations

Table whose rows are stimulus presentations (i.e. a given image, for a given duration, typically 250 ms) and whose columns are presentation characteristics. :rtype: pandas.DataFrame

stimulus_templates

A dictionary containing the stimulus images presented during the session keys are data set names, and values are 3D numpy arrays. :rtype: dict

stimulus_timestamps

Timestamps associated with stimulus presentations on the monitor (corrected for monitor delay). :rtype: numpy.ndarray

task_parameters

A dictionary containing parameters used to define the task runtime behavior. :rtype: dict

trials

A dataframe containing behavioral trial start/stop times, and trial data :rtype: pandas.DataFrame