Cable cell probing and sampling

Definitions

probe

A measurement that can be performed on a cell. Each cell kind will have its own sorts of probe. Cable cells (arbor.cable_probe) allow the monitoring of membrane voltage, total membrane current, mechanism state, and a number of other quantities, measured either over the whole cell, or at specific sites (see Cable cell probing and sampling).

vector probe

Certain probes work over a region rather than a locset. This means that, depending settings such as cv policy, data is sampled as a function of distance, yielding multiple data points. Such probes are distinguished from regular probes as “vector probes”.

probeset

A set of probes. Probes are placed on locsets, and therefore may describe more than one probe.

probeset address

Probesets are located at a probeset address, and the collection of probeset addresses for a given cell is provided by the recipe object. One address may correspond to more than one probe: as an example, a request for membrane voltage on a cable cell at sites specified by a locset expression will generate one probe for each site in that locset expression.

See Cable cell probing and sampling for a list of objects that return a probeset address.

probeset id

A designator for a probeset as specified by a recipe. The probeset id is a cell_member referring to a specific cell by gid, and the index into the list of probeset addresses returned by the recipe for that gid.

metadata

Each probe has associated metadata describing, for example, the location on a cell where the measurement is being taken, or other such identifying information. Metadata for the probes associated with a probeset id can be retrieved from the simulation object, and is also provided along with any recorded samples.

sampler
sample_recorder

A sampler is something that receives probeset data. It amounts to setting a particular probeset to a particular measuring schedule, and then having a handle with which to access the recorded probeset data later on.

sample

A record of data corresponding to the value at a specific probe at a specific time.

handle

A handle for reaching sampling data associated to a sampler, which is associated to a probeset. Setting a sampler (through simulation.sample()) returns handles. Sampled data can be retrieved by passing the handle associated to a sampler (associated to a probeset) to simulation.samples().

schedule

An object representing a series of monotonically increasing points in time, used for determining sample times (see Recipes).

Spiking

Threshold detectors have a dual use: they can be used to record spike times, but are also used in propagating signals between cells. See also threshold detector and 2. Threshold detectors..

API