ndx-franklab-novela Extension for NWB

About

ndx-franklab-novela is a python package containing NWB custom extensions for Loren Frank's Lab.

How to install

Add ndx-franklab-novela to your conda environment:

pip install ndx-franklab-novela

Or install the latest version from the repository:

pip install git+git://github.com/LorenFrankLab/ndx-franklab-novela

The original published extension maintained by NovelaNeuro can be installed using:

conda install -c conda-forge -c novelakrk ndx-franklab-novela

Dependencies

This extension uses the ndx-optogenetics extension. Installing ndx-franklab-novela will install the latest version of ndx-optogenetics from PyPI. Loading ndx-franklab-novela by importing ndx_franklab_novela will also load ndx_optogenetics.

Extensions

AssociatedFiles

Representation of associated files in NWB.

Attributes:

• description string: description of associated file
• content string: content of associated file
• task_epochs string: id of epochs with task that is descripted by associated files

HeaderDevice

Representation of HeaderDevice in NWB.

Attributes:

• headstage_serial string: headstage_serial from header global configuration
• headstage_smart_ref_on string: headstage_smart_ref_on from header global configuration
• realtime_mode string: realtime_mode from header global configuration
• headstage_auto_settle_on string: headstage_auto_settle_on from header global configuration
• timestamp_at_creation string: timestamp_at_creation from header global configuration
• controller_firmware_version string: conntroller_firmware_version from header global configuration
• controller_serial string: conntroller_serial from header global configuration
• save_displayed_chan_only string: save_displayed_chan_only from header global configuration
• headstage_firmware_version string: headstage_firmware_version from header global configuration
• qt_version string: qt_version from header global configuration
• compile_date string: compile_date from header global configuration
• compile_time string: compile_time from header global configuration
• file_prefix string: file_prefix from header global configuration
• headstage_gyro_sensor_on string: headstage_gyro_sensor_on from header global configuration
• headstage_mag_sensor_on string: headstage_mag_sensor_on from header global configuration
• trodes_version string: trodes_version from header global configuration
• headstage_accel_sensor_on string: headstage_accel_sensor_on from header global configuration
• commit_head string: commit_head from header global configuration
• system_time_at_creation string: system_time_at_creation from header global configuration
• file_path string: file_path from header global configuration

ShanksElectrode

Representation of electrodes of a shank in NWB.

Attributes:

• name string: name of the shank
• rel_x float: the rel_x value of this electrode
• rel_y float: the rel_y value of this electrode
• rel_z float: the rel_z value of this electrode

Shank

Representation of a shank in NWB.

Attributes:

• name string: name of the shank
• shanks_electrodes dict: electrodes in the shank

Probe

Representation of a probe in NWB.

Attributes:

• id int: unique id of the probe
• probe_type string: type of probe
• units string: units in device
• probe_description string: description of probe
• contact_side_numbering bool: Whether the electrodes were numbered in a scheme wherein the contacts were electrodes facing up toward the viewer (true) or if the numbering was based on the electrodes facing down (false). This is relevant when the goal is to determine where in the tissue each electrode contact is located. (optional)
• contact_size float: value of contact size as float
• shanks dict: shanks in the probe

DataAcqDevice

Representation of data acquisition device in NWB.

Attributes:

• system string: system of device
• amplifier string: amplifier (optional)
• adc_circuit string: adc_circuit (optional)

CameraDevice

Representation of a camera device in NWB.

Attributes:

• meters_per_pixel float: meters per pixel
• model string: model of this camera device
• lens string: info about lens in this camera
• camera_name string: name of this camera
• frame_rate float: frame rate of this camera (optional)

FrankLabOptogeneticEpochsTable

An extension of the OptogeneticEpochsTable from ndx-optogenetics with the following columns:

Columns:

• epoch_name string: name of this epoch
• epoch_number int: 1-indexed number of this epoch
• convenience_code string: convenience code of this epoch
• epoch_type string: type of this epoch
• theta_filter_on bool: whether the theta filter was on (optional)
• theta_filter_lockout_period_in_samples int: lockout period in samples for theta filter (optional)
• theta_filter_phase_in_deg float: phase in degrees for theta filter (optional)
• theta_filter_reference_ntrode int: reference ntrode for theta filter (optional)
• spatial_filter_on bool: whether the spatial filter was on (optional)
• spatial_filter_lockout_period_in_samples int: lockout period in samples for spatial filter (optional)
• spatial_filter_region_node_coordinates_in_pixels float, shape (n_region, n_nodes, 2,): If the spatial filter was used, the (x, y) coordinate of each boundary-defining node for each region. Note: all regions must have the same number of nodes. For regions with fewer nodes, use (-1, -1) to fill the additional xy values.'
• spatial_filter_cameras_index int: index column for spatial filter cameras (optional)
• spatial_filter_cameras : references to CameraDevice objects used for spatial filter (optional)
• spatial_filter_cameras_cm_per_pixel float: cm per pixel for spatial filter cameras (optional)
• ripple_filter_on bool: whether the ripple filter was on (optional)
• ripple_filter_lockout_period_in_samples int: lockout period in samples for ripple filter (optional)
• ripple_filter_threshold_sd float: threshold in standard deviations for ripple filter (optional)
• ripple_filter_num_above_threshold int: number of tetrodes above threshold for ripple filter (optional)
• speed_filter_on bool: Whether the speed filter was on. Closed-loop stimulation based on whether the animal is moving fast/slow enough. (optional)
• speed_filter_threshold_in_cm_per_s float: If the speed filter was used, the threshold for detecting a fast/slow animal (optional)
• speed_filter_on_above_threshold bool: If the speed filter was used, True if active when speed above threshold. (optional)
• stimulus_signal TimeSeries: Timeseries of the delivered stimulus. Can be continuous values or time of digital on/off events.

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This extension was created using ndx-template.