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NDI-matlab

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Installation
Tutorials
Tutorials
- 1 The NDI model
  1 The NDI model
  - 1.1 Introduction
  - 1.2 Real world vocabulary
- 2 Analzying your first electrophysiology experiment with NDI
  2 Analzying your first electrophysiology experiment with NDI
- 3 Tutorials for new coders or new Matlab users
  3 Tutorials for new coders or new Matlab users
  - 3.1 Newbie version of your first electrophysiology experiment with NDI
- 7 Writing your own apps and calculations
  7 Writing your own apps and calculations
  - 7.2 Writing short calculations
- Planned
  Planned
Document reference
Document reference
- ndi_document
- ndi_document_animalsubject
- ndi_document_app
- ndi_document_element
- ndi_document_element_epoch
- ndi_document_epochid
- ndi_document_projectvar
- ndi_document_subject
- ndi_document_subjectmeasurement
- apps
  apps
  - calculations
    calculations
    
    simple_calc
  - jrclust
    jrclust
    
    jrclust_clusters
  - markgarbage
    markgarbage
    
    valid_interval
  - spikeextractor
    spikeextractor
    
    spike_extraction_parameters
    
    spike_extraction_parameters_modification
    
    spiketimes
    
    spikewaves
  - spikesorter
    spikesorter
    
    sorting_parameters
    
    spike_clusters
  - spikesorter_hengen
    spikesorter_hengen
    
    extraction_parameters
    
    mountainsort_parameters
    
    neuron_hengen
    
    probe_geometry
  - vhlab_voltage2firingrate
    vhlab_voltage2firingrate
    
    binnedspikeratevm
    
    vmneuralresponseresiduals
    
    vmspikefilteringparameters
    
    vmspikefit
    
    vmspikesummary
- daq
  daq
- data
  data
  - fitcurve
  - ndi_document_binaryseries
- neuron
  neuron
  - neuron_extracellular
- newdoctemplate
  newdoctemplate
  - ndi_document_newdoctemplate
- stimulus
  stimulus
  - control_stimulus_ids
  - stimulus_presentation
  - stimulus_response
  - stimulus_response_scalar
  - stimulus_response_scalar_parameters
  - stimulus_response_scalar_parameters_basic
  - stimulus_tuningcurve
  - vision
    vision
    
    oridir
    oridir
    
    orientation_direction_tuning
Code reference
Code reference
- ndi_Init
- ndi_install
- ndi PACKAGE
  ndi PACKAGE
  - ndi.app
  - ndi.cache
  - ndi.calculation
  - ndi.database
  - ndi.document
  - ndi.documentservice
  - ndi.element
  - ndi.filesep
  - ndi.globals
  - ndi.ido
  - ndi.neuron
  - ndi.probe
  - ndi.query
  - ndi.session
  - ndi.subject
  - ndi.validate
  - ndi.version
  - app PACKAGE
    app PACKAGE
    
    ndi.app.appdoc
    
    ndi.app.markgarbage
    
    ndi.app.oridirtuning
    
    ndi.app.spikeextractor
    
    ndi.app.spikesorter
    
    ndi.app.spikesorter_hengen
    
    stimulus PACKAGE
    stimulus PACKAGE
    
    ndi.app.stimulus.decoder
    
    ndi.app.stimulus.tuning_response
  - calc PACKAGE
    calc PACKAGE
    
    example PACKAGE
    example PACKAGE
    
    ndi.calc.example.simple
  - daq PACKAGE
    daq PACKAGE
    
    ndi.daq.daqsystemstring
    
    ndi.daq.metadatareader
    
    ndi.daq.reader
    
    ndi.daq.system
    
    metadatareader PACKAGE
    metadatareader PACKAGE
    
    ndi.daq.metadatareader.NewStimStims
    
    reader PACKAGE
    reader PACKAGE
    
    ndi.daq.reader.mfdaq
    
    mfdaq PACKAGE
    mfdaq PACKAGE
    
    ndi.daq.reader.mfdaq.blackrock
    
    ndi.daq.reader.mfdaq.cedspike2
    
    ndi.daq.reader.mfdaq.intan
    
    ndi.daq.reader.mfdaq.spikegadgets
    
    system PACKAGE
    system PACKAGE
    
    ndi.daq.system.mfdaq
    
    premature FOLDER
    premature FOLDER
    
    ndi.daq/premature.ndi_daqsystem_image
    
    ndi.daq/premature.ndi_daqsystem_image_tiffstack
    
    ndi.daq/premature.ndi_image
    
    ndi.daq/premature.ndi_image_tiffstack
  - data PACKAGE
    data PACKAGE
    
    ndi.data.evaluate_fitcurve
  - database PACKAGE
    database PACKAGE
    
    ndi.database.binarydoc
    
    fun PACKAGE
    fun PACKAGE
    
    ndi.database.fun.createGenBankControlledVocabulary
    
    ndi.database.fun.createNIFbrainareas
    
    ndi.database.fun.databasehierarchyinit
    
    ndi.database.fun.docs2graph
    
    ndi.database.fun.findalldependencies
    
    ndi.database.fun.finddocs_missing_dependencies
    
    ndi.database.fun.ndi_document2ndi_object
    
    ndi.database.fun.opendatabase
    
    ndi.database.fun.plotinteractivedocgraph
    
    ndi.database.fun.projectvardef
    
    ndi.database.fun.readGenBankNames
    
    ndi.database.fun.readGenBankNodes
    
    implementations PACKAGE
    implementations PACKAGE
    
    binarydoc PACKAGE
    binarydoc PACKAGE
    
    ndi.database.implementations.binarydoc.matfid
    
    database PACKAGE
    database PACKAGE
    
    ndi.database.implementations.database.matlabdumbjsondb
    
    ndi.database.implementations.database.postgresdb
  - docs PACKAGE
    docs PACKAGE
    
    ndi.docs.all_documents2markdown
    
    ndi.docs.build
    
    ndi.docs.document2markdown
    
    ndi.docs.schemastructure2docstructure
  - element PACKAGE
    element PACKAGE
    
    ndi.element.timeseries
  - epoch PACKAGE
    epoch PACKAGE
    
    ndi.epoch.epochprobemap
    
    ndi.epoch.epochprobemap_daqsystem
    
    ndi.epoch.epochset
    
    ndi.epoch.findepochnode
    
    epochset PACKAGE
    epochset PACKAGE
    
    ndi.epoch.epochset.param
  - example PACKAGE
    example PACKAGE
    
    tutorial PACKAGE
    tutorial PACKAGE
    
    ndi.example.tutorial.plottreeshrewdata
    
    ndi.example.tutorial.tutorial_02_01
    
    ndi.example.tutorial.tutorial_02_02
    
    ndi.example.tutorial.tutorial_02_03
    
    ndi.example.tutorial.tutorial_02_04
    
    ndi.example.tutorial.tutorial_02_05
  - file PACKAGE
    file PACKAGE
    
    ndi.file.navigator
    
    navigator PACKAGE
    navigator PACKAGE
    
    ndi.file.navigator.epochdir
  - fun PACKAGE
    fun PACKAGE
    
    ndi.fun.check_Matlab_toolboxes
    
    ndi.fun.convertoldnsd2ndi
    
    ndi.fun.run_Linux_checks
    
    ndi.fun.stimulustemporalfrequency
  - globals PACKAGE
    globals PACKAGE
    
    ndi.globals.assert
  - gui PACKAGE
    gui PACKAGE
    
    ndi.gui.Data
    
    ndi.gui.Icon
    
    ndi.gui.Lab
    
    ndi.gui.gui
    
    ndi.gui.gui_v2
  - neuron PACKAGE
    neuron PACKAGE
    
    ndi.neuron.hengen
  - probe PACKAGE
    probe PACKAGE
    
    ndi.probe.timeseries
    
    fun PACKAGE
    fun PACKAGE
    
    ndi.probe.fun.probestruct2probe
    
    ndi.probe.fun.probetype2objectinit
    
    timeseries PACKAGE
    timeseries PACKAGE
    
    ndi.probe.timeseries.mfdaq
    
    ndi.probe.timeseries.stimulator
  - session PACKAGE
    session PACKAGE
    
    ndi.session.dir
    
    ndi.session.mock
    
    ndi.session.sessiontable
  - setup PACKAGE
    setup PACKAGE
    
    ndi.setup.angeluccilab
    
    ndi.setup.dbkatzlab
    
    ndi.setup.marderlab
    
    ndi.setup.vhlab
    
    daq PACKAGE
    daq PACKAGE
    
    metadatareader PACKAGE
    metadatareader PACKAGE
    
    ndi.setup.daq.metadatareader.AngelucciStims
    
    reader PACKAGE
    reader PACKAGE
    
    mfdaq PACKAGE
    mfdaq PACKAGE
    
    stimulus PACKAGE
    stimulus PACKAGE
    
    ndi.setup.daq.reader.mfdaq.stimulus.angelucci_visstim
    
    ndi.setup.daq.reader.mfdaq.stimulus.vhlabvisspike2
    
    system PACKAGE
    system PACKAGE
    
    ndi.setup.daq.system.angeluccilab
    
    ndi.setup.daq.system.dbkatzlab
    
    ndi.setup.daq.system.marderlab
    
    ndi.setup.daq.system.vhlab
    
    epoch PACKAGE
    epoch PACKAGE
    
    ndi.setup.epoch.epochprobemap_daqsystem_vhlab
  - test PACKAGE
    test PACKAGE
    
    ndi.test.cache
    
    app PACKAGE
    app PACKAGE
    
    ndi.test.app.markgarbage
    
    ndi.test.app.spikeextractor
    
    daq PACKAGE
    daq PACKAGE
    
    ndi.test.daq.blackrock
    
    ndi.test.daq.build_intan_flat_exp
    
    ndi.test.daq.intan_flat
    
    ndi.test.daq.intan_flat_metadata
    
    ndi.test.daq.intan_flat_saved
    
    ndi.test.daq.sg_flat
    
    ndi.test.daq.test_ndi_device_image_tiffstack
    
    ndi.test.daq.test_ndi_image_tiffstack_multipleepoch
    
    database PACKAGE
    database PACKAGE
    
    ndi.test.database.test_ndi_document
    
    ndi.test.database.test_ndi_document_jsons
    
    ndi.test.database.test_ndi_validate
    
    ndi.test.database.testpostgresdb
    
    ndi.test.database.testpostgresdb2
    
    ndi.test.database.testpostgresdbsearch
    
    core PACKAGE
    core PACKAGE
    
    ndi.test.database.core.test_ndi_daq_documents
    
    ndi.test.database.core.test_ndi_daqreader_documents
    
    ndi.test.database.core.test_ndi_daqsystem_documents
    
    ndi.test.database.core.test_ndi_filenavigator_documents
    
    ndi.test.database.core.test_ndi_syncgraph_documents
    
    ndi.test.database.core.test_ndi_syncrule_documents
    
    debug PACKAGE
    debug PACKAGE
    
    ndi.test.debug.ndi_debug_database_stats
    
    element PACKAGE
    element PACKAGE
    
    ndi.test.element.test_ndi_element
    
    filenavigator PACKAGE
    filenavigator PACKAGE
    
    ndi.test.filenavigator.test_ndi_filenavigator
    
    ndi.test.filenavigator.test_ndi_filenavigator_fileIDfunction
    
    misc PACKAGE
    misc PACKAGE
    
    ndi.test.misc.bytestream_save
    
    ndi.test.misc.bytestream_test
    
    probe PACKAGE
    probe PACKAGE
    
    ndi.test.probe.test_ndi_probe
    
    session PACKAGE
    session PACKAGE
    
    ndi.test.session.ndi_test_sessiontable
    
    setup PACKAGE
    setup PACKAGE
    
    ndi.test.setup.angeluccilab
    
    ndi.test.setup.dbkatzlab_narendra
    
    ndi.test.setup.marderlab_hamood
    
    testsuite PACKAGE
    testsuite PACKAGE
    
    ndi.test.testsuite.ndi_testsuite
    
    time PACKAGE
    time PACKAGE
    
    ndi.test.time.filefind
    
    tutorial PACKAGE
    tutorial PACKAGE
    
    ndi.test.tutorial.tutorial_02_set
  - time PACKAGE
    time PACKAGE
    
    ndi.time.clocktype
    
    ndi.time.syncgraph
    
    ndi.time.syncrule
    
    ndi.time.timemapping
    
    ndi.time.timereference
    
    ndi.time.timeseries
    
    syncrule PACKAGE
    syncrule PACKAGE
    
    ndi.time.syncrule.commontriggers
    
    ndi.time.syncrule.filefind
    
    ndi.time.syncrule.filematch
FAQ
Contributing
Development schedule
Learning Matlab

ndi.docs.all_documents2markdown¶

  ALL_DOCUMENTS2MARKDOWN - write all NDI document types to documentation folder

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