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| --- | ||
| layout: default | ||
| title: Data structure and format | ||
| parent: Data structure | ||
| nav_order: 2 | ||
| --- | ||
| # Data loaders | ||
| {: .no_toc} | ||
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| ## Table of contents | ||
| {: .no_toc .text-delta } | ||
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| 1. TOC | ||
| {:toc} | ||
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| ## Raw data | ||
| CellExplorer supports raw binary data files (.dat files). This format is also supported by IntanTech, OpenEphys, KiloSort, Phy, NeuroSuite, Spyking Circus, NeuroSuite, Klustakwik, and many other tools. | ||
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| data = LoadBinary | ||
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| ## LFP data | ||
| CellExplorer also uses a basename.lfp file - A low-pass filtered and down-sampled raw data file for lfp analysis (for efficient data analysis and data storage; typically down-sampled to 1250Hz). The lfp file is automatically generated in the pipeline from the raw data file - using the script ce_LFPfromDat). The sampling rate is specified in the session struct (session.extracellular.srLfp). The LFP file has the same channel count and scaling as the dat file. | ||
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| data = LoadBinary | ||
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| ## General functions | ||
| loadStruct | ||
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| saveStruct | ||
| saveStruct(chanCoords,'channelInfo','session',session); | ||
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| ## Analog traces | ||
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| loadIntanAnalog | ||
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| ## Digital data | ||
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| loadIntanDigital | ||
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| loadOpenEphysDigital | ||
| ## Session metadata | ||
| sessionTemplate | ||
| loadSession | ||
| gui_session | ||
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| The session struct can be generated using the sessionTemplate.m and inspected with gui_session.m. The basename.session.mat files should be stored in the basepath. It is structured as defined below: | ||
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| ## Spikes | ||
| A MATLAB struct spikes stored in a .mat file: basename.spikes.cellinfo.mat. It can be generated with loadSpikes.m. The processing module ProcessCellMetrics.m used the script loadSpikes.m, to automatically load spike-data from either KiloSort, Phy or Neurosuite and saves it to a spikes struct. basename.spikes.cellinfo.mat is saved to the basepath. The struct has the following fields: | ||
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| loadSpikes.m | ||
| spikes = loadSpikes('session',session); | ||
| spikes = getWaveformsFromDat(spikes,session); | ||
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| Load spikes takes spike sorted formats from various algorithms: | ||
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| ## Monosynaptic connections | ||
| mono_res = ce_MonoSynConvClick(spikes,'includeInhibitoryConnections',true/false); % detects the monosynaptic connections | ||
| gui_MonoSyn(mono_res) % Shows the GUI for manual curation | ||
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| ## Cell metrics | ||
| loadCellMetrics | ||
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| bsasepaths = {'sessionName1','sessionName2','sessionName3'}; | ||
| cell_metrics = loadCellMetricsBatch('basepaths',bsasepaths); | ||
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| nwb = saveCellMetrics2nwb(cell_metrics,nwb_file); | ||
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| saveCellMetrics(cell_metrics,nwb_file) | ||
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| cell_metrics = ProcessCellMetrics('session', session); | ||
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| ## Events | ||
| This is a data container for event data. A MATLAB struct eventName stored in a .mat file: basename.eventName.events.mat with the following fields: | ||
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| loadEvents | ||
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| ## Manipulations | ||
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| ## Channels | ||
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| ## Time series | ||
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| StateExplorer | ||
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| ## States | ||
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| ## Behavior | ||
| This is a data container for behavioral tracking data. A MATLAB struct behaviorName stored in a .mat file: basename.behaviorName.behavior.mat with the following fields: | ||
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| loadOptitrack | ||
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| ## Trials | ||
| A MATLAB struct trials stored in a .mat file: basename.trials.behavior.mat. The trials struct is a special behavior struct centered around behavioral trials. trials has the following fields: | ||
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| ## Firing rate maps | ||
| This is a data container for firing rate map data. A MATLAB struct ratemap containing 1D or linearized firing rat maps, stored in a .mat file: basename.ratemap.firingRateMap.mat. The firing rate maps have the following fields: | ||
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| ## Intracellular time series | ||
| This is a data container for intracellular recordings. Any MATLAB struct intracellularName containing intracellular data would be stored in a .mat file: basename.intracellularName.intracellular.mat. It contains fields inherited from timeSeries with the following fields |