Neo
Docs (link), paper (link).
21 flashcards · Other · by lakesare
What is electrophysiology?
Electrical properties of CELLS and biological TISSUES
What exactly is a membrane potential?
Difference between: outside voltage inside voltage in the cell. Membrane potential (also transmembrane potential or membrane voltage) is the difference in electric potential between the interior and the exterior of a biological cell. Typical values of membrane potential are in the range –70 mV to –40 mV.
Name 3 electrophysiology data formats.
Spike2 NeuroExplorer Igor Pro Neo is a Python package for working with electrophysiology data in Python, together with support for reading a wide range of neurophysiology file formats, including Spike2, NeuroExplorer, AlphaOmega, Axon, Blackrock, Plexon, Tdt, Igor Pro, and support for writing to a subset of these formats plus non-proprietary formats including Kwik and HDF5. The goal of Neo is to improve interoperability between Python tools for analyzing, visualizing and generating electrophysi…
What is a Single-unit recording?
When we measure electro-physiological response from a single neuron. In neuroscience, single-unit recordings provide a method of measuring the electro-physiological responses of a single neuron using a microelectrode system.
Name 2 uses of microelectrodes. Microelectrode array.
to record neural signals to stimulate a neuron A microelectrode is very small size terminal used in electrophysiology for either recording of neural signals or electrical stimulation of nervous tissue. Historically, they were produced from pulled glass pipettes. More recent technology introduced the use of insulated metal wires. A microelectrode is an electrode used in electrophysiology either for recording neural signals or for the electrical stimulation of nervous tissue (they were first deve…
What is a channel?
A single recording site. A channel is a single recording site, usually a metal electrode tip or a metal pad on a silicon electrode. Glass pipettes are big and are hard to put close together, but one can record with multiple glass pipettes (just more unusual). These sites record electric fields. Each recording site (channel) also needs a unique analog input on a digital acquisition device (DAQ), which is also called a channel (one speaks of analog input channels). The DAQ has its own numbering s…
What's: 3 segments VS 8 channels?
3 segment - 3 trials A Segment may contain any of the data object types provided all the objects share a common clock, i.e., they represent data recorded at the same time, although the sampling interval, onset and duration of recording may differ between data objects.8 channels - 8 recording sites In this example we suppose that we have recorded from an 8-channel probe, and that we have recorded three trials/episodes. We therefore have a total of 8 x 3 = 24 signals, grouped into three AnalogSig…
Visually imagine a tetrode.
A tetrode is a type of electrode used in neuroscience for electrophysiological recordings. They are generally used to record the extracellular field potentials from nervous tissue, e.g. the brain. Tetrodes are constructed by bundling together four very small electrodes; each wire is generally less than 30 μm in diameter.
What tetrodes are usually used for?
To determine the spikes of individual neuron. Tetrodes are used to classify extra-cellular action potentials into sets generated by the individual neurons, as each channel of the tetrode is usually close enough to a cell such that action potentials emitted by that cell are detected on each of the four channels, but because of the spatial distribution of the individual channels, the amplitude of the signal varies across the four channels. Clustering techniques involve both examining the waveform…
What is spike sorting?
Multiple waveforms → activity of a single neuron. Spike sorting algorithms use the shape(s) of waveforms collected with one or more electrodes in the brain to distinguish the activity of one or more neurons from background electrical noise. Spike sorting is the process of detecting and classifying high-frequency deflections ("spikes") on a group of physically nearby recording channels.
People talking analogy: some people talk very loudly
Raw data isolate the spikes group spikes together based on similarity of amplitude divide by amplitude we could use accent, too! PCA!
[Principal Component Analysis] What's a good analogy for PCA?
Taking a photo of data! The graphics obtained from Principal Components Analysis provide a quick way to get a “photo” of the multivariate phenomenon under study. At its heart, performing a Principal Component Analysis involves taking a data table that contains the information about a certain phenomenon, in order to transform such data into a set of visual representations in some optimal sense. During the transformation process part of the information is “lost”. However, PCA seeks to minimize th…
Visually imagine signal averaging.
Signal averaging takes N signals with noise and derives a signal without noise. A set of N raw trials composed of a signal and significant noise component can be used to obtain an average with an enhanced signal-to-noise ratio. Signal averaging is a technique that allows estimation of signals that are buried in noise.Averaging is applied to enhance a time-locked signal component in noisy measurements. One possible representation of such a signal is as measurement x consisting of a signal s and…
When do the objects "share the common clock"?
Same recording starts time, recording ends time. A Segment may contain any of the data object types provided all the objects share a common clock, i.e., they represent data recorded at the same time, although the sampling interval, onset and duration of recording may differ between data objects.
Visually imagine AnalogSignal.
4 channels, 8 samples For example, let's say you have recordings from a tetrode containing 4 separate channels. In previous versions of Neo, we had :class:`AnalogSignal` for one-dimensional (single channel) signals, and :class:`AnalogSignalArray` for two-dimensional (multi-channel) signals. In Neo 0.5.0, these have been merged under the name :class:`AnalogSignal`. :class:`AnalogSignal` has the same behaviour as the old :class:`AnalogSignalArray`.
How does Neo decide whether to create: 1 AnalogSignal with multiple channels VS many AnalogSignals?
If same length, same units → 1 AnalogSignal. Previously, when reading multiple related signals (same length, same units) from a file, some IO classes would by default create a separate, single-channel :class:`AnalogSignal` per signal, others would combine all related signals into one multi-channel :class:`AnalogSignal`.From Neo 0.9.0, the default for all IO classes is to create a one multi-channel :class:`AnalogSignal`.
What's: gain VS offset?
gain - multiplies signal by a constant factor. Gain multiplies your signal by a constant factor.offset - adds a constant factor to your signal. Offset adds or subtracts a constant value to your signal.
In Neo: 'event' channel VS 'marker' channel
'event' channel - always '1' 'marker' channel - 'marker code' DATA is a multiple-column vector; the first column has the time of the event. The remaining columns indicate the marker code. In the case of 'events', this is just 1. If more than one channel is requested, DATA is returned as a cell array, one entry per channel.
In what format is data returned from neo.readevents_epochsamples('marker')?
1st column: time 2nd column: ['marker code', 'marker code', 'marker code'] DATA is a multiple-column vector; the first column has the time of the event. The remaining columns indicate the marker code. In the case of 'events', this is just 1. If more than one channel is requested, DATA is returned as a cell array, one entry per channel.
In what format is data returned from neo.readevents_epochsamples('event')?
1st column: time 2nd column: [1, 1, 1] DATA is a multiple-column vector; the first column has the time of the event. The remaining columns indicate the marker code. In the case of 'events', this is just 1. If more than one channel is requested, DATA is returned as a cell array, one entry per channel.
Which of these is unique: channel.name channel.id channel.index?
channel.name channel.id channel.index There are 3 ways to select a subset of channels: by index (0 based), by id or by name. By index is unambiguous 0 to n-1 (included), whereas for some IOs channel_names (and sometimes channel_ids) have no guarantees to be unique. In such cases, using names or ids may raise an error.