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NDI-matlab
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
2.1 Reading an example dataset
2.2 Automating data reading with NDI
2.3 Using apps to analyze data (example - spike sorting)
2.4 Analyzing spiking responses and tuning curve properties
2.5 Searching NDI databases
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 calculators
7 Writing your own apps and calculators
7.2 Writing short calculations
Planned
Planned
4. Case studies in reading data in NDI
5. Making your own data pipeline in NDI
6. Making your own analysis app that uses NDI
7. Submitting your data to an archive
8. Search and analyze NDI databases on the web
Document reference
Document reference
animalsubject
app
base
dataset_session_info
demoNDI
element
element_epoch
epochid
mock
projectvar
session
subject
subjectmeasurement
apps
apps
calculators
calculators
simple_calc
tuningcurve_calc
jrclust
jrclust
jrclust_clusters
markgarbage
markgarbage
valid_interval
spikeextractor
spikeextractor
spike_extraction_parameters
spike_extraction_parameters_modification
spikewaves
spikesorter
spikesorter
sorting_parameters
spike_clusters
vhlab_voltage2firingrate
vhlab_voltage2firingrate
binnedspikeratevm
vmneuralresponseresiduals
vmspikefilteringparameters
vmspikefit
vmspikesummary
daq
daq
daqmetadatareader
daqreader
daqreader_ndr
daqsystem
filenavigator
syncgraph
syncrule
data
data
binaryseries_parameters
fitcurve
ngrid
ingestion
ingestion
daqmetadatareader_epochdata_ingested
daqreader_epochdata_ingested
daqreader_mfdaq_epochdata_ingested
epochfiles_ingested
syncrule_mapping
metadata
metadata
openminds
openminds_element
openminds_stimulus
openminds_subject
neuron
neuron
neuron_extracellular
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.calculator
ndi.database
ndi.dataset
ndi.document
ndi.documentservice
ndi.element
ndi.filesep
ndi.globals
ndi.ido
ndi.neuron
ndi.pipeline
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
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
stimulus PACKAGE
stimulus PACKAGE
ndi.calc.stimulus.tuningcurve
cloud PACKAGE
cloud PACKAGE
ndi.cloud.calculate_document_size
ndi.cloud.create_cloud_metadata_struct
ndi.cloud.delete_cloud_openminds_doc
ndi.cloud.delete_local_openminds_doc
ndi.cloud.download_dataset
ndi.cloud.test_auth
ndi.cloud.test_datasets
ndi.cloud.test_documents
ndi.cloud.test_files
ndi.cloud.test_upload
ndi.cloud.test_upload_old
ndi.cloud.uilogin
ndi.cloud.update_cloud_metadata
ndi.cloud.update_cloud_metadata_struct
ndi.cloud.upload_dataset_database
api PACKAGE
api PACKAGE
documents PACKAGE
documents PACKAGE
ndi.cloud.api.documents.add_document
auth PACKAGE
auth PACKAGE
ndi.cloud.auth.confirmation_resend
ndi.cloud.auth.login
ndi.cloud.auth.logout
ndi.cloud.auth.password
ndi.cloud.auth.password_forgot
ndi.cloud.auth.verify
datasets PACKAGE
datasets PACKAGE
ndi.cloud.datasets.delete_datasetId
ndi.cloud.datasets.get_branches
ndi.cloud.datasets.get_datasetId
ndi.cloud.datasets.get_files
ndi.cloud.datasets.get_files_raw
ndi.cloud.datasets.get_organizations
ndi.cloud.datasets.get_published
ndi.cloud.datasets.get_unpublished
ndi.cloud.datasets.post_branch
ndi.cloud.datasets.post_bulk_delete
ndi.cloud.datasets.post_datasetId
ndi.cloud.datasets.post_organization
ndi.cloud.datasets.post_publish
ndi.cloud.datasets.post_submit
ndi.cloud.datasets.post_unpublish
documents PACKAGE
documents PACKAGE
ndi.cloud.documents.delete_documents
ndi.cloud.documents.get_documents
ndi.cloud.documents.get_documents_summary
ndi.cloud.documents.post_documents
ndi.cloud.documents.post_documents_update
files PACKAGE
files PACKAGE
ndi.cloud.files.get_files
ndi.cloud.files.get_files_raw
ndi.cloud.files.put_files
fun PACKAGE
fun PACKAGE
ndi.cloud.fun.check_metadata_cloud_inputs
ndi.cloud.fun.create_new_dataset
ndi.cloud.fun.find_instance_name
ndi.cloud.fun.find_techniques_names
ndi.cloud.fun.load_author_from_cloud
ndi.cloud.fun.load_dataType_from_cloud
ndi.cloud.fun.load_metadata_from_cloud
ndi.cloud.fun.make_dataset_from_docs_files
ndi.cloud.fun.search_id
internal PACKAGE
internal PACKAGE
ndi.cloud.internal.decode_jwt
ndi.cloud.internal.get_token_expiration
ndi.cloud.internal.get_uploaded_document_ids
ndi.cloud.internal.get_uploaded_file_ids
users PACKAGE
users PACKAGE
ndi.cloud.users.get_user
ndi.cloud.users.post_user
ndi.cloud.users.post_user_update
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.ndr
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
ndi.database.ingestion_help
app PACKAGE
app PACKAGE
dataset_viewer PACKAGE
dataset_viewer PACKAGE
utility PACKAGE
utility PACKAGE
ndi.database.app.dataset_viewer.utility.listLocalDatasets
ndi.database.app.dataset_viewer.utility.listRemoteDatasets
fun PACKAGE
fun PACKAGE
ndi.database.fun.NDICloud_essential_metadata_submit
ndi.database.fun.calculate_size_in_cloud
ndi.database.fun.check_metadata_inputs
ndi.database.fun.copy_session_to_dataset
ndi.database.fun.copydocfile2temp
ndi.database.fun.createGenBankControlledVocabulary
ndi.database.fun.createNIFbrainareas
ndi.database.fun.create_new_database
ndi.database.fun.database2json
ndi.database.fun.databasehierarchyinit
ndi.database.fun.dataset_metadata
ndi.database.fun.docs2graph
ndi.database.fun.docs_from_ids
ndi.database.fun.extract_docs_files
ndi.database.fun.find_ingested_docs
ndi.database.fun.findalldependencies
ndi.database.fun.finddocs_missing_dependencies
ndi.database.fun.load_metadata_to_GUI
ndi.database.fun.ndi_document2ndi_object
ndi.database.fun.ndicloud_ontology_lookup
ndi.database.fun.openMINDSobj2ndi_document
ndi.database.fun.openMINDSobj2struct
ndi.database.fun.opendatabase
ndi.database.fun.plotinteractivedocgraph
ndi.database.fun.projectvardef
ndi.database.fun.readGenBankNames
ndi.database.fun.readGenBankNodes
ndi.database.fun.read_presentation_time_structure
ndi.database.fun.scan_for_upload
ndi.database.fun.upload_to_NDI_cloud
ndi.database.fun.write_presentation_time_structure
implementations PACKAGE
implementations PACKAGE
binarydoc PACKAGE
binarydoc PACKAGE
ndi.database.implementations.binarydoc.matfid
database PACKAGE
database PACKAGE
ndi.database.implementations.database.didsqlite
ndi.database.implementations.database.matlabdumbjsondb
ndi.database.implementations.database.matlabdumbjsondb2
ndi.database.implementations.database.postgresdb
fun PACKAGE
fun PACKAGE
ndi.database.implementations.fun.doc2ingesteddbfilename
ndi.database.implementations.fun.expell
ndi.database.implementations.fun.expell_plan
ndi.database.implementations.fun.ingest
ndi.database.implementations.fun.ingest_plan
internal PACKAGE
internal PACKAGE
ndi.database.internal.list_binary_files
metadata_app PACKAGE
metadata_app PACKAGE
ndi.database.metadata_app.convertFormDataToDocuments
ndi.database.metadata_app.getRequiredFields
checker PACKAGE
checker PACKAGE
ndi.database.metadata_app.checker.subject
class PACKAGE
class PACKAGE
ndi.database.metadata_app.class.Affiliation
ndi.database.metadata_app.class.AffiliationData
ndi.database.metadata_app.class.AuthorData
ndi.database.metadata_app.class.DatasetData
ndi.database.metadata_app.class.DatasetVersionData
ndi.database.metadata_app.class.DeviceType
ndi.database.metadata_app.class.Electrode
ndi.database.metadata_app.class.ElectrodeArray
ndi.database.metadata_app.class.License
ndi.database.metadata_app.class.MiscellaneousProbe
ndi.database.metadata_app.class.Organization
ndi.database.metadata_app.class.Pipette
ndi.database.metadata_app.class.Probe
ndi.database.metadata_app.class.ProbeData
ndi.database.metadata_app.class.Species
ndi.database.metadata_app.class.SpeciesData
ndi.database.metadata_app.class.Strain
ndi.database.metadata_app.class.Subject
ndi.database.metadata_app.class.SubjectData
ndi.database.metadata_app.class.test
fun PACKAGE
fun PACKAGE
ndi.database.metadata_app.fun.SearchSpecies
ndi.database.metadata_app.fun.add_to_database
ndi.database.metadata_app.fun.checkValidRORID
ndi.database.metadata_app.fun.expandDropDownItems
ndi.database.metadata_app.fun.generateShortName
ndi.database.metadata_app.fun.getCCByLicences
ndi.database.metadata_app.fun.getOpenMindsInstances
ndi.database.metadata_app.fun.getOpenmindsInstanceFile
ndi.database.metadata_app.fun.getOrcId
ndi.database.metadata_app.fun.getOrcIdSearchUrl
ndi.database.metadata_app.fun.getPublicationTitleFromDoi
ndi.database.metadata_app.fun.getPubmedIdFromDoi
ndi.database.metadata_app.fun.getRorId
ndi.database.metadata_app.fun.getRorIdSearchUrl
ndi.database.metadata_app.fun.getSpeciesInfo
ndi.database.metadata_app.fun.loadExperimentalApproach
ndi.database.metadata_app.fun.loadInstancesToListBox
ndi.database.metadata_app.fun.loadInstancesToTreeCheckbox
ndi.database.metadata_app.fun.loadOpenMindsInstanceCatalog
ndi.database.metadata_app.fun.loadProbes
ndi.database.metadata_app.fun.loadSubjects
ndi.database.metadata_app.fun.loadTechniquesEmployed
ndi.database.metadata_app.fun.loadUnits
ndi.database.metadata_app.fun.loadUserInstanceCatalog
ndi.database.metadata_app.fun.loadUserInstances
ndi.database.metadata_app.fun.mustBeValidDate
ndi.database.metadata_app.fun.parseOpenMINDSAtID
ndi.database.metadata_app.fun.resolveRelatedPublication
ndi.database.metadata_app.fun.saveUserInstances
ndi.database.metadata_app.fun.submit_dataset
dataset PACKAGE
dataset PACKAGE
ndi.dataset.dir
docs PACKAGE
docs PACKAGE
ndi.docs.all_documents2markdown
ndi.docs.build
ndi.docs.calcbuild
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
ndi.file.pfilemirror
ndi.file.temp_fid
ndi.file.temp_name
navigator PACKAGE
navigator PACKAGE
ndi.file.navigator.epochdir
type PACKAGE
type PACKAGE
ndi.file.type.mfdaq_epoch_channel
fun PACKAGE
fun PACKAGE
ndi.fun.assertAddonOnPath
ndi.fun.channelname2prefixnumber
ndi.fun.check_Matlab_toolboxes
ndi.fun.console
ndi.fun.convertoldnsd2ndi
ndi.fun.find_calc_directories
ndi.fun.plot_extracellular_spikeshapes
ndi.fun.pseudorandomint
ndi.fun.run_Linux_checks
ndi.fun.stimulustemporalfrequency
ndi.fun.timestamp
calc PACKAGE
calc PACKAGE
ndi.fun.calc.stimulus_tuningcurve_log
stimulus PACKAGE
stimulus PACKAGE
ndi.fun.stimulus.f0_f1_responses
ndi.fun.stimulus.tuning_curve_to_response_type
globals PACKAGE
globals PACKAGE
ndi.globals.assert
gui PACKAGE
gui PACKAGE
ndi.gui.Data
ndi.gui.Icon
ndi.gui.Lab
ndi.gui.docViewer
ndi.gui.gui
ndi.gui.gui_v2
component PACKAGE
component PACKAGE
ndi.gui.component.CommandWindowProgressMonitor
ndi.gui.component.NDIProgressBar
abstract PACKAGE
abstract PACKAGE
ndi.gui.component.abstract.ProgressMonitor
internal PACKAGE
internal PACKAGE
ndi.gui.component.internal.AsynchProgressTracker
ndi.gui.component.internal.ProgressTracker
event PACKAGE
event PACKAGE
ndi.gui.component.internal.event.MessageUpdatedEventData
ndi.gui.component.internal.event.ProgressUpdatedEventData
utility PACKAGE
utility PACKAGE
ndi.gui.utility.centerFigure
mock PACKAGE
mock PACKAGE
ndi.mock.ctest
fun PACKAGE
fun PACKAGE
ndi.mock.fun.clear
ndi.mock.fun.stimulus_presentation
ndi.mock.fun.stimulus_response
ndi.mock.fun.subject_stimulator_neuron
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.empty_id
ndi.session.mock
ndi.session.sessiontable
setup PACKAGE
setup PACKAGE
ndi.setup.angeluccilab
ndi.setup.dbkatzlab
ndi.setup.marderlab
ndi.setup.vhlab
ndi.setup.yangyangwang
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
ndi.setup.daq.system.yangyangwang
epoch PACKAGE
epoch PACKAGE
ndi.setup.epoch.epochprobemap_daqsystem_vhlab
stimulus PACKAGE
stimulus PACKAGE
vhlab PACKAGE
vhlab PACKAGE
ndi.setup.stimulus.vhlab.add_stimulus_approach
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.all_doc_fields
ndi.test.database.load_all_docs
ndi.test.database.test_ndi_document
ndi.test.database.test_ndi_document_jsons
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
dataset PACKAGE
dataset PACKAGE
ndi.test.dataset.manual
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
gui PACKAGE
gui PACKAGE
ndi.test.gui.displayDocViewer
ingest PACKAGE
ingest PACKAGE
ndi.test.ingest.compare
ndi.test.ingest.mfdaq
ndi.test.ingest.mfdaq_compare
ndi.test.ingest.syncgraph
misc PACKAGE
misc PACKAGE
ndi.test.misc.bytestream_save
ndi.test.misc.bytestream_test
pipeline PACKAGE
pipeline PACKAGE
ndi.test.pipeline.edit
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
fun PACKAGE
fun PACKAGE
ndi.time.fun.samples2times
ndi.time.fun.times2samples
syncrule PACKAGE
syncrule PACKAGE
ndi.time.syncrule.commontriggers
ndi.time.syncrule.filefind
ndi.time.syncrule.filematch
util PACKAGE
util PACKAGE
ndi.util.choosefile
ndi.util.choosefileordir
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ndi.cloud.test_auth
ndi.cloud.test_auth is a script.