Skip to content
NDI-matlab
ndi.daq/premature.ndi_image_tiffstack
Initializing search
GitHub
NDI-matlab
GitHub
Home
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 calculations
7 Writing your own apps and calculations
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
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
ndi_document_daqmetadatareader
ndi_document_daqreader
ndi_document_daqsystem
ndi_document_filenavigator
ndi_document_syncgraph
ndi_document_syncrule
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.daq/premature.ndi_image_tiffstack
¶