# Glossary :::{glossary} Action potential A characteristic signal that appears in excitable cell membranes, which takes the form of an electric potential difference waveform that propagates down the length of the cell membrane. In neurons, these indicate neuron activation. See {term}`Spike`. Basket cell A type of inhibitory neuron whose synaptic output targets the cell body and proximal dendrites of excitatory neurons. Many basket cells express the molecular marker parvalbumin (PV), but not all basket cells are PV+: some express molecules such as cholecystokinin (CCK). PV basket cells are typically fast spiking compared to other neurons and are thought to be important for gain control of network activity and setting the temporal precision of network activity. Bipolar cell A subset of VIP cell with a bipolar dendritic arbor. See {term}`VIP cell`. BCI Brain Computer Interface A method of controlling a computer signal through the activity of a neuron. This can be extended to other types of devices (e.g. joysticks or robotic arms). This is also often referred to as "Brain Machine Interface" CCF Common Coordinate Framework The [CCF](background/CCF.md) is a a standard 3D reference space for the mouse brain that enables spatial integration of data across modalities. ChR2 Channelrhodopsin A light-gated ion channel used in the field of optogenetics to control neuronal activity with light. Container *There is no consistent use of this term* Most often this refers to the set of recording sessions for a single ophys imaging plane, but can also refer to the set of sessions for an animal. Cre line The Cre-lox system is a site-specific recombinase technology. Cre-recombinase is a tyrosine site-specific recombinase that catalyzes the recombination of DNA between specific sites known as loxP sequences. As used in these experiments, Cre is used with loxP {term}`Reporter line` in order to drive recombinase of the loxP sites and drive the expression of the reporter. As Cre is often expressed within a specific gene, this allows the reporter expression to be restricted to particular subset of cells. For specific lines used, see the section on [transgenic tools](background/transgenic-tools.md). Dataset *There is no consistent use of this term* Driver line A general term for transgenic mouse lines that are engineered to label a specific cell type or cell population by expressing a specific gene under the control of the promoter for the cell type or cell population of interest. A {term}`Cre line` is a common type of Driver line that allows specific genes to be expressed when crossed with a {term}`reporter line`. The driver line determines what cell population is targeted, and the reporter line determines what will be expressed in that specific cell population (for example, GFP, GCaMP, or Channelrhodopsin). Ephys Shorthand for electrophysiology. Experiment *There is no consistent use of this term* It can refer to a stimulus protocol, an entire data collection campaign, or a single session. It is highly ambiguous. Fast spiking neuron FSN FSI Fast spiking neurons are so called because of their "narrow," fast action potentials, specifically as seen in intracellular recordings of a cell in response to a prolonged step of current. Additionally, with sufficient current injection fast spiking neurons exhibit fast spike rates, and do not show frequency adaptation, or slowing of spike rates, over time. In unlabeled extracellular recordings, units with narrow action potentials are also referred to as fast spiking neurons. This feature is sometimes used to putatively label neurons with narrow spikes as particular cell types, such as {term}`PV+ neuron`s, among others. Fluorophore A type of molecule which absorb light and re-emit it at a longer wavelength in a process called fluorescence. As a result, fluorophores fluoresce only while exposed to a light source. GABA Gamma-aminobutyric acid (GABA) is the main inhibitory neurotransmitter in the mammalian brain. In cortex, most GABAergic neurons are local interneurons. Genetically-encoded calcium indicator GECI A protein expressed by a cell that will change its fluorescence upon binding to a Ca{sup}`2+` ion. Used to visualize neural activity with fluorescence microscopy. GCaMP A family of {term}`GECI`. GCaMP was generated by a fusion of the calcium binding domain of the calmodulin protein with green fluorescent protein (GFP). In these data we use primarily GCaMP6f as well as some GCaMP6s, fast and slow variants respectively. These two variants differ in their sensitivity as well as their kinetics — primarily with regards to their decay. For more see {cite:t}`chen2013`. GFP Green fluorescent protein. Discovered at FHL. Higher visual area HVA A **higher visual area** is a term for cortical visual areas that receive input from the primary visual cortex, thus considered to be "higher" in the visual hierarchy. In primates, higher visual areas include V2, V3, V4, V5, MT, etc. In the mouse, higher visual areas include: VISl, VIsal, VISpm, VISam, VISrl among others. For more, see {cite:t}`glickfeld_higher-order_2017`. Hyperparameter A free parameter that controls behaviors in machine learning algorithms. These are distinct from parameters which control behaviors of the models developed by the algorithms; hyperparameters affect how the algorithm finds the models in the first place. Interneuron Also known as a local interneuron: a neuron that has short axons and synapse exclusively with nearby neurons. In the cortex the term is often used to refer to inhibitory neurons. Interspike interval ISI The interspike interval is the the time between two sequential action potentials (spikes) of a neuron. The ISI is used in the quality control of spike-sorting for ephys experiments, assuring that spikes assigned to a unit don't fall within the refactory period of the neuron (a few milliseconds), indicating that there is contaimination between units.. ISI is also used to characterize firing patterns of neurons. Intrinsic signal imaging ISI Intrinsic signal imaging, also called ISI, is a method to measure changes in blood flow associated with neural activity using reflectance of red light on the brain's surface, measured using a standard CCD camera. The amount of red light reflected by the brain tissue increases when oxygenated hemoglobin perfuses the local region. The timecourse of the ISI signal is slow, and the magnitude of the reflectance changes are small. As a result, the use of periodic stimuli can aid in signal detection. A common use of ISI is to map {term}`retinotopy` across the brain surface by moving a slowly drifting bar across the visual field then measuring the signal in each pixel at the frequency of the periodic drifting bar. ISI has also been used to identify orientation maps in species with organized orientation maps like cats and primates, as well as to map the location of the whisker barrels in somatosensory cortex of the mouse. For additional papers using ISI to map the organization of the mouse visual cortex see {cite:t}`kalatsky2003` and {cite:t}`garrett2014`. Local field potential LFP Transient electrical potential generated in nervous tissue by the summed activity of cells in that tissue. This is typically measured in a lower temporal-frequency band of less than 250 Hz. Martinotti cell A Martinotti cell is a particular subtype of SST cell that targets the apical dendrites of pyramidal cells in layer 1. Martinotti cells are found in layer 2/3 and layer 5. Minnie column A colloquial name for the 100 micron by 100 micron square column of cortex targeted for the census across layers. This column is a particularly well proofread collection of cells. Minnie dataset A colloquial name for the millimeter-scale MICrONs electron microscopy dataset. NWB Neurodata Without Borders A standardized file format for physiology and behavior data. All of our physiology and behavior data is stored in NWB files. The Visual Coding and Visual Behavior data are in NWB files with a hdf backend, while the newer data (V1DD, BCI, Dynamic Foraging, NP Ultra & Psychedelics) have a Zarr backend - which is optimized for cloud access. More info can be found [here](https://nwb.org/) Neurogliaform cell A type of interneuron that makes a diffuse axonal arbor and is thought to release {term}`GABA` through both synaptic release and volume transmission, non-selectively inhibiting neurons nearby. Neuropixels A family of devices for obtaining high channel count single unit extracellular recordings created through a collaborative open science project funded by Howard Hughes Medical Institute, Gatsby Charitable Trust, the Wellcome Trust, and the Allen Institute. These devices utilize modern integrated circuit design to miniaturize aspects of electrophysiology, enabling recordings of hundred of single units from a single probe with minimal brain damage. {cite:t}`jun2017` describes these probes; a summary can also be found [here](background/neuropixels-description). Ophys Shorthand for optical physiology, often in reference to {term}`Two-photon calcium imaging`, but can also include other methods such as fiber photometry. Optogenetics A method for controlling the activity of neurons by expressing light activated ion channels (using a {term}`reporter line` ) in a specific subpopulation of cells (using a {term}`Driver line`) to enable temporally precise control of neural spiking. Spiking can be suppressed or enhanced using different types of reporters. See {cite:t}`peron2011` for a review on optogenetics as a method. Optotagging A technique that uses {term}`optogenetics` in order to identify neurons that belong to a specific subpopulation. See: [Optotagging](background/Optotagging). Parvalbumin-positive interneuron PV+ neuron Fast spiking neurons, also known as fast spiking interneurons, is a short-hand for parvalbumin positive GABA-ergic inhibitory interneurons found in many brain regions that have strong inhibitory effects on neighboring cells. In experimental preparations where the genetic identity of neurons can be paired with electrophysiological recordings, PV+ neurons have short action potentials, occasionally less than 400 µS. Primary visual cortex V1 VISp The largest visual area in cortex that receives inputs from the Lateral geniculate nucleus of thalamus. Often referred to as V1 or VISp. Pyramidal cell A type of excitatory neuron with a characteristic cell body shape and apical dendrite. In visual cortex, pyramidal cells are by far the most common type of excitatory neuron. Receptive field In a sensory context, the receptive field of a neuron is the region of the stimulus domain in which sensory stimulus needs to lie in order to evoke a response. For visual cortical cells, for example, the receptive field is the region of visual space in which stimuli can evoke neural responses. In a computational context, this notion is often generalized multiple dimensions (e.g. space, time, frequency, etc.) and thus equates to the necessary stimulus features that drive neural response (e.g. a localized grating of a specific orientation and frequency). Regular Spiking neuron RS Neurons that, when injected with a long step of current in the context of intracellular recordings, show spike frequency adaptation where the rate of spiking decreases over time. These neurons also have longer (or wider) action potentials, and lower spike rates even when injected with large currents due to hyperpolarization after each action potential. These are the most common type of neurons in the mammalian cortex, and are often associated excitatory neurons. In extracellular recordings, neurons with longer action potentials are also sometimes referred to as regular spiking neurons, a feature which is used to associate these units with specific cell types, such as excitatory pyramidal neurons among others. Reporter An exogenous coding region joined to a promoter sequence or element in an expression vector that is introduced into cells to provide the means for measuring the promoter activity [source](https://www.promega.com/resources/guides/cell-biology/bioluminescent-reporters/#:~:text=What%20is%20a%20Reporter%20Gene,for%20measuring%20the%20promoter%20activity.). Reporter line A reporter line is a transgenic mouse line that is engineered to express a specific protein that enables monitoring or manipulation of neural activity (such as GFP, GCaMP, or Channelrhodopsin) under the control of cre or FLP recombinase, or a tetracycline transactivator system. The gene engineered into the reporter line will not be expressed unless the protein that controls reporter gene expression (such as cre or FLP) is present, such as by breeding a mouse from the reporter line with a mouse from a specific {term}`Driver line` that expresses the control protein. Injecting a virus that delivers cre or FLP in a cell type specific manner can also trigger the expression of the reporter gene. Retinotopy retinotopic map retinotopy refers to the mapping of visual space on to neural space. Most visual areas of the brain contain an orderly map of visual space such that neighboring regions in space are represented by neighboring regions in the brain. Retinotopic maps are typically measured in terms of altitude (aka vertical retinotopy), referring to the axis from upper to lower visual field, and and azimuth (aka horizontal retinotopy), referring to the axis from left to right in space. ROI A region of interest is a general term that describes a subregion of an image. When used in reference to two photon calcium imaging, an ROI is the mask containing pixels thought to belong to a single neuron. Saccade A rapid and ballistic eye movement that shifts the visual field between two fixation points. Mice are not foveal animals, and their eye movements are different from foveal animals (such as humans). Session A physiological and/or behavioral recording that happens at one time. Skeleton A linear tree-like structure that defines the shape of a neuron. Somatostatin cell A type of inhibitory interneuron expressing the molecular marker somatostatin (SST, or sometimes SOM). SST cells tend to target the distal dendrites of excitatory neurons, and have important roles in regulating the activity of excitatory neurons. Spatial frequency How often sinusoidal components of as signal or structure repeat per unit of distance. When used in reference to drifting gratings, spatial frequency means the distance between the bars of the grating. Typically measured as cycles per degree. Targeted structure The brain region where data was collected from. Temporal frequency How many complete periods the signal goes through for a given unit of time. Typically measured in Hertz. Transgenic line A mouse line whose genome has been altered by the introduction of one or more foreign DNA sequences. For these contexts, this typical involves using {term}`Cre line`s to drive the expression of a {term}`Reporter line` within a specific subset of cells. Two-photon calcium imaging A term for techniques which measure neural activity of neurons by measuring a fluorescent calcium indicator. These indicators are usually a protein expressed in a cell, such as {term}`GCaMP`, often using a specific combination of {term}`Driver line` and {term}`reporter line`s to express GCaMP in a specific subset of neurons. Fluorescent dyes can also be used to perform calcium imaging. At rest a neuron has low levels of calcium, and when the neuron spikes calcium flows into the neuron and raises the level of calcium, which binds to the calcium indicator and increases the emitted fluorescence in a specific wavelength. See {cite:t}`svoboda2006` for a review of two-photon calcium imaging. Unit A putative neuron in extracellular electrophysiology, with varying degrees of confidence assigned to it. In extracellular electrophysiology, neurons are referred to as *units*, because we cannot guarantee that all the spikes assigned to one unit actually originate from a single cell. Unlike in two-photon imaging, where you can visualize each neuron throughout the entire experiment, with electrophysiology we can only “see” a neuron when it fires a spike. If a neuron moves relative to the probe, or if it’s far away from the probe, some of its spikes may get mixed together with those from other neurons. Because of this inherent ambiguity, quality metrics allow you to find the right units for your analysis. Even highly contaminated units can contain potentially valuable information about brain states, but certain types of analysis require more stringent quality thresholds to ensure that all of the included units are well isolated from their neighbors. VIP cell A type of inhibitory interneuron expressing the molecular marker Vasoactive Intestinal Protein. VIP cells tend to target {term}`Somatostatin cell`s rather than excitatory neurons. This role as a "disinhibitory specialist" is thought to be important for context-dependent modulation of cortical activity. Many VIP cells have a characteristic bipolar axon that points along the axis of the cortical column and are thus often called "bipolar cells". Waveform Spike In a system neuroscience setting, this often refers to the voltage over time measured with an electrode when an individual neuron produces an action potential. :::