Common fields

Session, subject, stimulus, locomotion, and eye-tracking data use a common NWB organization and synchronized time base.

NameDescriptionFormatNWB Path
Session identityUnique file identifier, session identifier, description, and recording start time.Scalar text and datetime metadatanwbfile.identifier
nwbfile.session_id
nwbfile.session_start_time
Subject metadataMouse identifier, species, sex, age, date of birth, and genotype.Subject containernwbfile.subject
Acquisition devicesRegistered recording hardware; concrete device types differ by modality.Mapping of Device containersnwbfile.devices
Stimulus presentationsOne timestamped table per experimental, control, receptive-field, or movie block.TimeIntervals tablesnwbfile.intervals[table_name]
Stimulus timingDisplay-synchronized start and stop times for every presentation.Float columns in a dynamic tablenwbfile.intervals[table_name]["start_time"]
nwbfile.intervals[table_name]["stop_time"]
Stimulus parametersTrial identity and visual parameters such as orientation, contrast, duration, spatial frequency, and temporal frequency.Numeric and categorical table columnsnwbfile.intervals[table_name].to_dataframe()
Running speedLinear locomotion speed aligned to the session clock.Timestamped TimeSeries arraynwbfile.processing["running"]["running_speed"]
Wheel rotationUnwrapped wheel rotation aligned to running speed and stimulus timing.Timestamped TimeSeries arraynwbfile.processing["running"]["running_wheel_rotation"]
Eye fitsPupil, corneal-reflection, and eye-perimeter center, width, height, angle, raw area, cleaned area, and timestamps.Three DynamicTable objectsnwbfile.processing["eye_tracking"]["pupil"]
nwbfile.processing["eye_tracking"]["corneal_reflection"]
nwbfile.processing["eye_tracking"]["ellipse"]
Likely blinksBoolean likely-blink flag for each synchronized eye-camera sample.Boolean TimeSeriesnwbfile.processing["eye_tracking"]["likely_blink_times"]

Neuropixels-specific fields

Sorted units, probe/electrode anatomy, quality metrics, waveforms, and local field potentials.

NameDescriptionFormatNWB Path
Sorted unitsOne row per sorted unit with identity, probe, shank, firing properties, anatomical estimates, and quality metrics.Units dynamic tablenwbfile.units
Spike timesAll detected spike timestamps for each unit.Ragged float array per unitnwbfile.units["spike_times"][unit_row]
Mean waveformsAverage and standard-deviation spike waveforms across channels for each unit.Ragged multidimensional arraysnwbfile.units["waveform_mean"][unit_row]
nwbfile.units["waveform_sd"][unit_row]
Unit yield and activitySpike count, firing rate, firing range, amplitude, and median amplitude.Numeric dynamic-table columnsnwbfile.units[["num_spikes", "firing_rate", "amplitude"]]
Unit quality metricsPresence ratio, amplitude cutoff, ISI violations, SNR, d-prime, isolation distance, silhouette, refractory-period metrics, and default QC classification.Numeric and categorical table columnsnwbfile.units.to_dataframe()
Unit anatomical positionEstimated CCF coordinates, depth, probe, shank, and linked electrode region for each unit.Numeric columns and DynamicTableRegionnwbfile.units["electrodes"]
nwbfile.units[["estimated_x", "estimated_y", "estimated_z"]]
Electrode tableEvery recorded channel with probe group, channel name, anatomical location, physical scaling, relative position, and CCF coordinates.Electrodes DynamicTablenwbfile.electrodes
Probe groupsProbeA through ProbeF electrode groups linked to registered Neuropixels devices; the exact recorded subset varies by session.Mapping of ElectrodeGroup objectsnwbfile.electrode_groups
Local field potentialDownsampled voltage by channel and probe, with timestamps and electrode-region links.Probe-specific ElectricalSeries arraysnwbfile.processing["ecephys"]["LFP"]["ElectricalSeriesProbeA-LFP"]
Optotagging presentationsLaser timing and parameters for 5 Hz, 40 Hz, and raised-cosine photostimulation.TimeIntervals tablesnwbfile.intervals["5 hz pulse train_presentations"]

Mesoscope-specific fields

Eight VISp/VISl imaging planes with ROI masks, fluorescence products, inferred events, and field-of-view images.

NameDescriptionFormatNWB Path
Imaging planesFour VISp and four VISl planes with device, optical channel, indicator, excitation wavelength, imaging rate, cortical location, grid spacing, and field origin.Mapping of eight ImagingPlane containersnwbfile.imaging_planes
Plane processing modulesOne module per imaging plane linking all segmentation, trace, event, and image products.Eight ProcessingModule containersnwbfile.processing[plane]
ROI segmentationOne ROI row per segmented soma or dendrite, linked to its imaging plane and reference images.PlaneSegmentation dynamic tablenwbfile.processing[plane]["image_segmentation"]["roi_table"]
ROI image masksDense 512 x 512 weighted mask for every segmented ROI.ROI x height x width float arraynwbfile.processing[plane]["image_segmentation"]["roi_table"]["image_mask"]
ROI classificationsSoma/dendrite labels and corresponding classifier probabilities.Boolean and float table columnsnwbfile.processing[plane]["image_segmentation"]["roi_table"].to_dataframe()
Raw ROI fluorescenceMean fluorescence within each ROI before neuropil correction.Time x ROI RoiResponseSeriesnwbfile.processing[plane]["raw_timeseries"]["ROI_fluorescence_timeseries"]
Neuropil fluorescenceFluorescence measured in the surrounding neuropil and the separately stored neuropil-corrected trace.Two time x ROI RoiResponseSeries arraysnwbfile.processing[plane]["neuropil_fluorescence_timeseries"]
nwbfile.processing[plane]["neuropil_corrected_timeseries"]
dF/F tracesBaseline-normalized fluorescence for every ROI, stored in percent.Time x ROI RoiResponseSeries arraynwbfile.processing[plane]["dff_timeseries"]["dff_timeseries"]
Inferred eventsDeconvolved neural-event values for every ROI on the same timestamps as fluorescence.Time x ROI RoiResponseSeries arraynwbfile.processing[plane]["event_timeseries"]
Field-of-view imagesAverage projection, maximum projection, and segmentation-mask summary image for each plane.512 x 512 grayscale image setnwbfile.processing[plane]["images"]

SLAP2-specific fields

Modern files contain two DMD imaging paths with weighted source masks, dual-channel fluorescence, baseline and dF/F traces, and structural/activity images. Pilot-era layouts are intentionally omitted.

NameDescriptionFormatNWB Path
DMD imaging planesDMD1 and DMD2 optical paths with device, optical channel, indicator, excitation wavelength, imaging rate, and cortical location.Two ImagingPlane containersnwbfile.imaging_planes["ImagingPlane_DMD1"]
nwbfile.imaging_planes["ImagingPlane_DMD2"]
Source segmentationOne table per DMD path linking extracted synaptic or somatic sources to the corresponding imaging plane.Two PlaneSegmentation dynamic tablesnwbfile.processing["ophys"]["ImageSegmentation"]["PlaneSegmentation_DMD1"]
Weighted source masksRagged lists of source-pixel x/y coordinates and weights, indexed once per extracted source.Ragged compound pixel_mask arraynwbfile.processing["ophys"]["ImageSegmentation"]["PlaneSegmentation_DMD1"]["pixel_mask"]
Source axial boundsMinimum and maximum z indices associated with every extracted source.Integer dynamic-table columnsnwbfile.processing["ophys"]["ImageSegmentation"]["PlaneSegmentation_DMD1"][["z_min", "z_max"]]
Green-channel dF/FBaseline-normalized green-channel signal for each source, typically glutamate or voltage indicator fluorescence.Time x source RoiResponseSeriesnwbfile.processing["ophys"]["Fluorescence_DMD1"]["DMD1_dFF_green"]
Red-channel dF/FBaseline-normalized red-channel signal for each source, including the concurrently recorded reference or calcium channel.Time x source RoiResponseSeriesnwbfile.processing["ophys"]["Fluorescence_DMD1"]["DMD1_dFF_red"]
Baseline fluorescenceGreen- and red-channel F0 estimates corresponding to the source traces.Two time x source RoiResponseSeries arraysnwbfile.processing["ophys"]["Fluorescence_DMD1"]["DMD1_F0_green"]
nwbfile.processing["ophys"]["Fluorescence_DMD1"]["DMD1_F0_red"]
Mean imagesMean structural image for channel 0 and channel 1 in each DMD field of view.Single-frame grayscale image seriesnwbfile.processing["ophys"]["DMD1_mean_image_channel0"]
nwbfile.processing["ophys"]["DMD1_mean_image_channel1"]
Activity imageSource-localization activity projection for each DMD imaging path.Single-frame grayscale image seriesnwbfile.processing["ophys"]["DMD1_activity_image"]