NDI-Matlab and NDR-Matlab

30 flashcards · Biology · by lakesare

1. What does NDI stand for?

   Neuroscience Data Interface

2. What's in situ?

   In situ - in place, on site (latin) For example, in fields such as physics, geology, chemistry, or biology, in situ may describe the way a measurement is taken, that is, in the same place the phenomenon is occurring without isolating it from other systems or altering the original conditions of the test.

3. What does FAIR stand for?

   Findability, Accessibility, Interoperability, and Reuse. In 2016, the ‘FAIR Guiding Principles for scientific data management and stewardship’ were published in Scientific Data. The authors intended to provide guidelines to improve the Findability, Accessibility, Interoperability, and Reuse of digital assets.

4. [NDI terminology] Name 2 types of a probe. Probes are part of a broader class of experiment items that we term elements, which include not only concrete physical objects like probes but also inferred objects that are not observed directly, such as neurons in an extracellular recording experiment, or abstract quantities, such as simulated data, or a model of the information that an animal has about a stimulus at a given time.

   makes a measurement (e.g. EEG electrode) Examples of probes that make measurements include a whole cell pipette, a sharp electrode, a single channel extracellular electrode, multichannel electrodes with either known or unknown geometries, cameras, 2-photon microscopes, fMRI machines, nose-poke detectors, EMG electrodes, and EEG electrodes.provide simulation (e.g. audio speakers) Examples of probes that provide stimulation are odor ports, valve-driven interaural cannulae, food reward dispensers,…

5. [NDI terminology] What does DAQ stand for?

   Data AcQuisition system

6. [NDI terminology] What are these things probe is connected to: subject DAQ

   subject - e.g. experimental animal This subject can be an experimental research animal, a human subject, a set of cells in a dish, a test resistor, the air, a potato, anything, but it must be named and given an identifier in NDI.DAQ - records history of the probe. Data AcQuisition system.The second important connection of a probe is to a data acquisition system that stores the measurements or the stimulation history of the probe. We term such a system a DAQ system.

7. [NDI terminology] What interval of time is an epoch?

   [DAQ switched on; DAQ switched off] An epoch is an interval of time during which a DAQ system is switched on and then off to make a recording. An example experiment. A probe is any instrument that can make a measurement from or provide stimulation to a subject. In this case, an electrode with an amplifier is monitoring signals in the cerebral cortex of a ferret. The electrode is a probe, and the ferret is a subject. A DAQ system is an instrument that digitally logs the measurements or stimulus…

8. [NDI terminology] Give a database analogy for: probe VS element? Probes are part of a broader class of experiment items that we term elements, which include not only concrete physical objects like probes but also inferred objects that are not observed directly, such as neurons in an extracellular recording experiment, or abstract quantities, such as simulated data, or a model of the information that an animal has about a stimulus at a given time.

   probe - table element - view

9. [NDI terminology] Visually imagine probes VS elements.

   probes elements

10. Who is this?

    A shrew. Shrew is a small insectivorous mammal resembling a mouse, with a long pointed snout and tiny eyes.

11. [probemap.txt] When does the reference number change? This text file has all of the information needed to specify the probe and its connections.

    When the probe moves. It has a name for the probe that is meaningful to the user, and the reference specifies an identifier that groups the recordings of the probe. Typically, when the probe is in one physical position, the reference number is kept the same, but when the probe is moved (such as when an electrode is advanced), the reference number is incremented. This tells NDI to try to combine information from recordings that have the same name and reference

12. [probemap.txt] What object does the "stimulator" type create?

    ndi.probe.timeseries.stimulator https://raw.githubusercontent.com/VH-Lab/NDI-matlab/master/ndi_common/probe/probetype2object.json

13. [ndi.daq.system] ndi.daq.system consists of 3 components: ndi.file.navigator ndi.daq.reader ndi.daq.metadatareader

    ndi.file.navigator - finds the file associated with each epoch of data ndi.file.navigator object whose job it is to find the files or streams associated with each epoch of data.ndi.daq.reader an ndi.daq.reader object whose job it is to read the raw data from the files.ndi.daq.metadatareader ndi.daq.metadatareader (optionally) whose job is to read any metadata associated with the epoch (such as stimulus parameter information).

14. [ndi.daq.system] ndi.daq.system consists of 3 components: ndi.file.navigator ndi.daq.reader ndi.daq.metadatareader

    ndi.file.navigator ndi.file.navigator object whose job it is to find the files or streams associated with each epoch of data.ndi.daq.reader - read raw data an ndi.daq.reader object whose job it is to read the raw data from the files.ndi.daq.metadatareader ndi.daq.metadatareader (optionally) whose job is to read any metadata associated with the epoch (such as stimulus parameter information).

15. [ndi.daq.system] ndi.daq.system consists of 3 components: ndi.file.navigator ndi.daq.reader ndi.daq.metadatareader

    ndi.file.navigator ndi.file.navigator object whose job it is to find the files or streams associated with each epoch of data.ndi.daq.reader an ndi.daq.reader object whose job it is to read the raw data from the files.ndi.daq.metadatareader - read metadata ndi.daq.metadatareader (optionally) whose job is to read any metadata associated with the epoch (such as stimulus parameter information).

16. Name 2 ways to read data from files.

    ndi.daq.reader At the moment, NDI still uses its native ndi.daq.reader objects but soon it will be able to use any ndr.reader object, which will streamline the addition of new file formats.NDR-matlab Neuroscience Data ReadersIf you want to contribute an ndi.daq.reader for a new file format, please see our new project Neuroscience Data Readers NDR-matlab. We have spun off the job of reading raw neuroscience data files into this project to make it easier to contribute file readers and because som…

17. What's here: in blue in black?

    in blue - raw voltage recording in black - stimulus timing (1 - one stimulus, 2 - another) We wrote a short function so that you can see the raw voltage recording and the stimulus timing information. Each stimulus appears as a number and its duration is indicated by the black bar. You can pan with the mouse to scroll through the recording.

18. What does ndi.daq.system.mfdaq stand for?

    multifunction data acquisition We need to make new ndi.daq.system objects for our data acquisition system and our stimulator. Our devices are multifunction data acquisition systems, so we use the ndi.daq.system.mfdaq subtype.

19. [NDI-Matlab] Visually imagine 2 things a probe is connected to.

    subject DAQ system A probe is anything that measures or stimulates; one end of a probe is connected to a subject, and the other end of a probe is connected to a data acquisition device.

20. [NDI-Matlab] Name 2 ways to tell NDI how the probe is connected to subject and DAQ system.

    ndi.epoch.epochprobemap - in code We tell NDI how the probe is connected by creating an ndi.epoch.epochprobemap. Usually, we do this with a little code that instructs NDI how to read this information directly from the laboratory's own file information.ndi.epoch.epochprobemap_daqsystem - via tab-delimited file probemap.txtBut in this example, we will use the generic ndi.epoch.epochprobemap_daqsystem object, which reads in a simple tab-delimited text file.

21. [NDI-Matlab tutorial] Name 3 probes of the system from the NDI-matlab tutorial.

    n-trode for V1 neuron ndi.probe.timeseries.mfdaq object: { name: 'ctx' (cortex), type: 'n-trode' }n-trode for LGN neuron ndi.probe.timeseries.mfdaq object: { name: 'lgn', type: 'n-trode' }visual stimulator ndi.probe.timeseries.stimulator object: { name: 'vis_stim', type: 'stimulator' }

22. Give an example of ndi.app.

    ndi.app.spikeextractor (spike extractor) An app for our purposes is any application program that can read data from NDI and perform some analysis or computation on this data. Some apps exist outside of NDI, and know how to read data from NDI experiments and write results back to NDI experimental sessions. One example of such an app is the spike sorting program JRClust. Here, we will examine one of these apps that we made for spike extraction. Just like Windows computers come with NotePad and Ma…

23. What's the difference between these probes: electrode, tetrode NeuroPixel, NeuroNexus

    electrode, tetrode - few-channel electrodes NeuroPixel, NeuroNexus - many-channel electrodes ndi.app.spikeextractor is a plain-but-usable program for extracting spike waveforms from voltage records. It is suitable for spike extraction situations where the channel count for each electrode is low, such as single electrodes or tetrodes. It is not suitable for dense, multichannel electrodes like NeuroPixels or dense NeuroNexus probes.

24. [NDI terminology] Visually imagine ndi.session ndi.database ndi.document

    session.database = { document, document, ... } pseudocode Each ndi.session object has an ndi.database object as one of its properties. This database holds the ndi.document objects that contain the metadata and data results of calculations that apps and programs have performed on the original data.

25. [NWB] Visually imagine time series. The TimeSeries neurodata type defines how generic data values that change over time should be stored. In particular, the TimeSeries type must contain a description, an N-dimensional “data” dataset (array) where the first dimension is time, and either a 1-dimensional “timestamps” dataset or both a sampling rate and starting time.

    x-axis: timey-axis: some data points In mathematics, a time series is a series of data points indexed (or listed or graphed) in time order. Most commonly, a time series is a sequence taken at successive equally spaced points in time.

26. [NWB] What's timestamps_reference_time for?

    Time values are stored with reference to timestamps_reference_time. All time values in a TimeSeries and other neurodata types must be stored in seconds relative to the timestamps_reference_time value, a datetime value stored at the root of the NWB file. By default, this is the same as the session_start_time, another datetime value stored at the root of the NWB file.

27. [NWB] What does NWB stand for?

    Neurodata Without Borders Neurodata Without Borders (NWB) is a data standard for neurophysiology, providing neuroscientists with a common standard to share, archive, use, and build analysis tools for neurophysiology data. NWB is designed to store a variety of neurophysiology data, including data from intracellular and extracellular electrophysiology experiments, data from optical physiology experiments, and tracking and stimulus data.

28. How do we specify, for each epoch: which probe maps to which DAQ channel.

    usually we have to manually specify the mapping Commonly, this information must be specified manually using a data type that we have created.sometimes the mapping is available in file metadata But some multifunction DAQs (such as SpikeGadgets MFDAQs) and file formats include this epoch metadata in their native file formats, and this metadata can be processed from the files directly.

29. Visually imagine: metric time series event time series

    metrics - measurements gathered at regular time intervals events - measurements gathered at irregular time intervals E.g. logs

30. Visually imagine an old-school Data Acquisition System (DAQ).

    A technician writing down temperatures on a piece of paper is performing data acquisition.