NWB Format Specification Release 2.4.0 Aug 12, 2021 Table of contents I Introduction1 1 Overview 3 1.1 neurodata_type : Assigning types to specifications........................4 1.2 NWBContainer, NWBData, NWBDataInterface: Base neurodata_types for containers and datasets..................................................4 1.3 Time Series : A base neurodata_type for storing time series data.................4 1.4 Data Processing Modules: Organizing processed data..........................5 1.5 Extending the format...........................................5 1.5.1 Extending TimeSeries and NWBContainer...........................5 1.6 Common attributes............................................6 2 Comments and Definitions 7 2.1 Notation.................................................7 2.2 Storing Time Values...........................................8 2.3 Links and data references........................................8 2.4 Design notes...............................................8 2.5 Tables and ragged arrays.........................................9 2.6 Doubly ragged arrays.......................................... 11 2.7 References to rows of a table....................................... 12 II Format Specification 13 3 Format Overview 17 3.1 Namespace – NWB core......................................... 17 4 Type Specifications 19 4.1 Base data types.............................................. 19 4.1.1 NWBData............................................ 19 4.1.2 Image.............................................. 20 4.1.3 NWBContainer......................................... 21 4.1.4 NWBDataInterface....................................... 22 4.1.5 TimeSeries........................................... 23 4.1.5.1 Groups: sync...................................... 27 4.1.6 ProcessingModule....................................... 28 4.1.6.1 Groups: <NWBDataInterface>............................ 29 4.1.6.2 Groups: <DynamicTable>............................... 29 i 4.1.7 Images.............................................. 30 4.2 Devices.................................................. 31 4.2.1 Device.............................................. 31 4.3 Epochs.................................................. 32 4.3.1 TimeIntervals.......................................... 32 4.4 Image data................................................ 35 4.4.1 GrayscaleImage......................................... 35 4.4.2 RGBImage........................................... 36 4.4.3 RGBAImage.......................................... 37 4.4.4 ImageSeries........................................... 38 4.4.4.1 Groups: sync...................................... 43 4.4.5 ImageMaskSeries........................................ 44 4.4.5.1 Groups: sync...................................... 49 4.4.6 OpticalSeries.......................................... 50 4.4.6.1 Groups: sync...................................... 54 4.4.7 IndexSeries........................................... 56 4.4.7.1 Groups: sync...................................... 60 4.5 NWB:N file................................................ 61 4.5.1 ScratchData........................................... 61 4.5.2 NWBFile............................................ 62 4.5.2.1 Groups: /acquisition.................................. 65 4.5.2.2 Groups: /acquisition/<NWBDataInterface>...................... 65 4.5.2.3 Groups: /acquisition/<DynamicTable>........................ 65 4.5.2.4 Groups: /analysis................................... 67 4.5.2.5 Groups: /analysis/<NWBContainer>......................... 67 4.5.2.6 Groups: /analysis/<DynamicTable>.......................... 67 4.5.2.7 Groups: /scratch.................................... 67 4.5.2.8 Groups: /scratch/<NWBContainer>.......................... 68 4.5.2.9 Groups: /scratch/<DynamicTable>.......................... 68 4.5.2.10 Groups: /processing.................................. 68 4.5.2.11 Groups: /processing/<ProcessingModule>...................... 69 4.5.2.12 Groups: /stimulus................................... 69 4.5.2.13 Groups: /stimulus/presentation............................ 69 4.5.2.14 Groups: /stimulus/presentation/<TimeSeries>.................... 70 4.5.2.15 Groups: /stimulus/templates.............................. 70 4.5.2.16 Groups: /stimulus/templates/<TimeSeries>...................... 70 4.5.2.17 Groups: /general.................................... 70 4.5.2.18 Groups: /general/<LabMetaData>.......................... 73 4.5.2.19 Groups: /general/devices............................... 74 4.5.2.20 Groups: /general/devices/<Device>.......................... 74 4.5.2.21 Groups: /general/subject................................ 74 4.5.2.22 Groups: /general/extracellular_ephys......................... 74 4.5.2.23 Groups: /general/extracellular_ephys/<ElectrodeGroup>............... 75 4.5.2.24 Groups: /general/extracellular_ephys/electrodes................... 75 4.5.2.25 Groups: /general/intracellular_ephys......................... 77 4.5.2.26 Groups: /general/intracellular_ephys/<IntracellularElectrode>............ 77 4.5.2.27 Groups: /general/intracellular_ephys/sweep_table.................. 78 4.5.2.28 Groups: /general/optogenetics............................. 78 4.5.2.29 Groups: /general/optogenetics/<OptogeneticStimulusSite>............. 78 4.5.2.30 Groups: /general/optophysiology........................... 78 4.5.2.31 Groups: /general/optophysiology/<ImagingPlane>.................. 79 4.5.2.32 Groups: /intervals................................... 79 4.5.2.33 Groups: /intervals/epochs............................... 80 4.5.2.34 Groups: /intervals/trials................................ 80 ii 4.5.2.35 Groups: /intervals/invalid_times............................ 80 4.5.2.36 Groups: /intervals/<TimeIntervals>.......................... 80 4.5.2.37 Groups: /units..................................... 80 4.5.3 LabMetaData.......................................... 81 4.5.4 Subject............................................. 82 4.6 Miscellaneous neurodata_types...................................... 85 4.6.1 AbstractFeatureSeries...................................... 85 4.6.1.1 Groups: sync...................................... 88 4.6.2 AnnotationSeries........................................ 90 4.6.2.1 Groups: sync...................................... 94 4.6.3 IntervalSeries.......................................... 95 4.6.3.1 Groups: sync...................................... 99 4.6.4 DecompositionSeries...................................... 100 4.6.4.1 Groups: bands..................................... 104 4.6.4.2 Groups: sync...................................... 105 4.6.5 Units.............................................. 106 4.7 Behavior................................................. 112 4.7.1 SpatialSeries.......................................... 112 4.7.1.1 Groups: sync...................................... 115 4.7.2 BehavioralEpochs........................................ 117 4.7.2.1 Groups: <IntervalSeries>............................... 117 4.7.3 BehavioralEvents........................................ 118 4.7.3.1 Groups: <TimeSeries>................................ 118 4.7.4 BehavioralTimeSeries...................................... 119 4.7.4.1 Groups: <TimeSeries>................................ 119 4.7.5 PupilTracking.......................................... 120 4.7.5.1 Groups: <TimeSeries>................................ 120 4.7.6 EyeTracking........................................... 121 4.7.6.1 Groups: <SpatialSeries>................................ 121 4.7.7 CompassDirection....................................... 122 4.7.7.1 Groups: <SpatialSeries>................................ 122 4.7.8 Position............................................. 123 4.7.8.1 Groups: <SpatialSeries>................................ 123 4.8 Extracellular electrophysiology..................................... 124 4.8.1 ElectricalSeries......................................... 124 4.8.1.1 Groups: sync...................................... 128 4.8.2 SpikeEventSeries........................................ 130 4.8.2.1 Groups: sync...................................... 134 4.8.3 FeatureExtraction........................................ 136 4.8.4 EventDetection......................................... 138 4.8.5 EventWaveform......................................... 140 4.8.5.1 Groups: <SpikeEventSeries>............................. 140 4.8.6 FilteredEphys.......................................... 141 4.8.6.1 Groups: <ElectricalSeries>.............................. 141 4.8.7 LFP............................................... 142 4.8.7.1 Groups: <ElectricalSeries>.............................. 142 4.8.8 ElectrodeGroup......................................... 143 4.8.9 ClusterWaveforms....................................... 145 4.8.10 Clustering............................................ 147 4.9 Intracellular electrophysiology...................................... 149 4.9.1 PatchClampSeries........................................ 149 4.9.1.1 Groups: sync...................................... 154 4.9.2 CurrentClampSeries...................................... 155 4.9.2.1 Groups: sync...................................... 160 iii 4.9.3 IZeroClampSeries........................................ 161 4.9.3.1 Groups: sync...................................... 166 4.9.4 CurrentClampStimulusSeries.................................. 167 4.9.4.1 Groups: sync...................................... 171 4.9.5 VoltageClampSeries......................................