2. Description

Starting with definitions of many of the terms used in pCLAMP, this chapter contains information of a general nature likely to be useful for pCLAMP users. Middle sections in the chapter discuss electrophysiology terminology conventions, and there is a discussion of the theory behind sampling. The final two sections list pCLAMP file types and a range of pCLAMP “vital statistics”.

DEFINITIONS

A number of terms in standard use in Axon Instruments/Molecular Devices applications are defined below:

>

A waveform consists of a series of analog voltage steps, ramps and/or trains of pulses, or arbitrary data in a file, generated on an output signal in order to stimulate a cell. Also termed the “command waveform” or “stimulus waveform”, it can also have digital outputs associated with it.

> An epoch is a subsection of a waveform that can be defined as a step, ramp, or pulse train, and increased or decreased incrementally in amplitude and/or duration from sweep to sweep within a run.

>

A sample is the datum produced by one A/D (analog-to-digital) conversion or one D/A

(digital-to-analog) conversion. In analysis contexts, samples may be referred to as points

(see below).

> A sweep is the digitized data from all input signals for a defined number of samples. A sweep can contain up to one million samples, with all signals multiplexed at equal time intervals. A command waveform can be concurrently output during a sweep. Sweeps were known as episodes in older versions of pCLAMP. See Figure 2.1 for illustration of the relationship between runs, sweeps, channels and trials.

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A run is a set of sweeps. Sweeps within a run may all be the same, or they can be configured to have amplitude and/or duration changes from sweep to sweep. A run can contain up to 10,000 sweeps. If multiple runs are specified, all sets of sweeps are averaged together to produce a single averaged set of sweeps. See Figure 2.1 for illustration of the relationship between runs, sweeps, channels and trials.

> A trial is the data digitized from one or more runs, and saved as a single file. SeeFigure 2.1 for illustration of the relationship between runs, sweeps, channels and trials.

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2. Description

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Figure 2.1: Clampex data structure showing relationship between runs and trial.

> A trace is a continuous set of data samples from a single input signal. When data are displayed as sweeps, each trace represents a sweep within that signal.

>

A point is a single datum in a data file, similar to sample, above, although points can be created in a file without having been converted from an analog signal by an A/D converter.

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Definitions

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A channel is a physical connection through which analog and digital signals are received or transmitted. Channels are identified in pCLAMP by the name of the digitizer port where connection is made: e.g. Analog IN #0, Digital OUT #5.

> A signal is a set of name, unit, scale factor and offset, according to which:

a

Voltage inputs received at the analog input ports of the digitizer are represented in

Clampex as the physical parameter (unit) actually being read by the amplifier or transducer, with correct scaling and offset, and a user-selected name.

b

Voltage outputs generated through the digitizer’s analog output ports are represented in Clampex as the physical parameter (unit) actually being delivered to the preparation by the amplifier or transducer, with correct scaling and offset, and a userselected name.

In Clampex, numerous signals can be configured in association with each analog input and output channel (in the Lab Bench). A specific signal is assigned to a channel in the protocol configuration.

> A protocol is a set of configuration settings for a trial. It defines the acquisition mode, the trial’s hierarchy (i.e. the number of sweeps per run, and runs per trial), the sampling rate, the definition of the waveform, and many other options as well, which can all be saved into a *.pro protocol file.

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An experiment can be composed of several different protocols, and thus may result in several data files. In the context of sequencing keys where protocols can be assigned to keys and also linked to follow one another the *.sks files which define the keys and linkages can be said to define an experiment. Configurations created in the LTP

Assistant, which also result in *.sks files, are similarly called experiments.

> An event is a discrete response of biological activity, usually relatively short, within an input signal. It can be characterized by event detection, and extracted for further data analysis.

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The baseline in an episodic sweep consists of the initial and ending points of the trace, during which the holding level is output. Or, it is the level in an input signal that a trace maintains during periods that no events occur.

> A peak is a point in a trace of local maximum deviation from the baseline. Peaks can be positive (above the baseline) or negative (below the baseline).

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The rise is that part of the trace that, in an event, goes from the direction of the baseline to the peak. In the case of a negative peak, the rise is a downwards movement of the trace. In previous versions of pCLAMP, rising phases were sometimes referred to with the term left, as in “greatest left slope”.

> The decay is that part of the trace that, in an event, goes from the direction of the peak back to the baseline. In the case of a negative peak, the decay is an upwards movement of the trace. In previous versions of pCLAMP decay phases were sometimes referred to with the term right, as in “greatest right slope”.

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