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: is contact_side_numbering enabled
• 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_bottom_left_coord_in_pixels float, shape (2, ): bottom left coordinate in pixels for spatial filter (optional)
• spatial_filter_top_right_coord_in_pixels float, shape (2, ): top right coordinate in pixels for spatial filter (optional)
• 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)

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This extension was created using ndx-template.