Ephus: multipurpose data acquisition software for neuroscience experiments

Abstract

Physiological measurements in neuroscience experiments often involve complex stimulus paradigms and multiple data channels. Ephus (http://www.ephus.org) is an open-source software package designed for general-purpose data acquisition and instrument control. Ephus operates as a collection of modular programs, including an ephys program for standard whole-cell recording with single or multiple electrodes in typical electrophysiological experiments, and a mapper program for synaptic circuit mapping experiments involving laser scanning photostimulation based on glutamate uncaging or channelrhodopsin-2 excitation. Custom user functions allow user-extensibility at multiple levels, including on-line analysis and closed-loop experiments, where experimental parameters can be changed based on recently acquired data, such as during in vivo behavioral experiments. Ephus is compatible with a variety of data acquisition and imaging hardware. This paper describes the main features and modules of Ephus and their use in representative experimental applications.

Keywords: data acquisition; electrophysiology; imaging; mapping; software.

Figure 1

Ephus programs for management of general experimental information. (A) The hotswitch window provides many customizable buttons to rapidly switch between experimental configurations (e.g., family of current steps, synaptic circuit mapping) and program settings (e.g., video exposure time). Also visible are menu items to save or restore settings for individual programs, as well as all programs. The Copy settings menu item aids in sharing settings among lab members. This menu is available in every Ephus program. (B) The xsg program, responsible for binding data and header information from all programs and saving to disk, provides user controls for specifying the file-naming parameters and for indicating the start of a new experiment, or experimental epoch. (C) The autonotes program functions as an electronic laboratory notebook, automatically time-stamping text entries useful for recording experimental procedures. Some programs automatically add entries to this log (e.g., when a video image is captured, a hotswitch is pressed, or custom user functions are executed). Notes can also be entered manually in the text window. (D) Flowchart describing generic sequence of events during experiments.

Figure 2

Ephus software oscilloscope, displaying two amplifier acquisition channels simultaneously. (A) The scopeGui can display voltage or current signals from multiple amplifier channels simultaneously, each in a separate window (B,C), as well as the associated amplifier mode (VC, IC, IC0). Sweep and sampling rate are adjustable. A periodic test pulse can be toggled on or off, and its duration and amplitude adjusted. When in voltage-clamp mode, basic cell parameters (input resistance and capacitance) and recording parameters (pipette, series, and access resistance) can be monitored for a selected channel. (B) Live display of whole-cell pipette current in voltage-clamp mode for channel #1. (C) Live display of pipette current in voltage-clamp mode after seal formation for channel #2.

Figure 3

Ephus configuration for an in vitro electrophysiology experiment. Three Ephus programs coordinate to apply a family of current steps during a whole-cell recording. (A) ephys in external mode enables stimulation and acquisition on amplifier channel #1 in response to a trigger signal from loopGui. (B) loopGui triggers ephys, in 4-s intervals, for each pulse in the sequence defined by pulseJacker. (C) pulseJacker maps a sequence of pulse stimuli to individual amplifier channels. (D) The acquisition window displays the last record acquired, optionally overlaid with previously acquired records, as shown here for six sequential steps of increasing applied current.

Figure 4

qcam: user interface for video control and display. (A) Control panel for video acquisition parameters (exposure, temporal averaging, spatial binning), online display parameters (frame rate, look-up table, zoom), and storage parameters. (B) Live video display, obtained by running the qcam program in preview mode, of pyramidal neurons in a brain slice during a patch-clamp experiment (60× water-immersion objective, 58μm below surface of 300-μm thick sagittal slice in mouse motor cortex).

Figure 5

Ephus configuration for synaptic circuit mapping experiment. (A) The mapper program provides all controls necessary for scanning and flashing a laser beam across the sample in a specified grid pattern while simultaneously recording from one or more amplifier channels during each optical stimulus. Additional controls allow for calibrating a Pockels cell, calibrating transmitted laser power, selecting an appropriate grid pattern and adjusting its orientation, saving an image of the sample, marking the position of the recorded cell(s) in the field-of-view, and specifying the stimulation interval. Instead of a stimulation grid, the user can manually specify one or more positions at which to flash the sample. (B) An auxiliary window displaying the sample (in this case a sagittal slice of mouse motor cortex in 4× bright-field). The stimulation grid pattern is overlaid on the bright-field image and has been aligned (using the controls shown in A) to the pia and centered on the soma of the patched cell (blue circle). The red circle indicates the location of the last stimulus delivered. This display updates throughout the mapping procedure. (C) Voltage-clamp recording acquired during the last stimulus, showing a complex synaptic response, followed by a voltage step for monitoring recording parameters. (D) A standard user function performs a rapid analysis of the whole-cell recording (see C) and provides immediate feedback on the ongoing map in the form of a pseudo-color plot. This display updates throughout the mapping procedure. Note that this online display does not distinguish between direct (evident here in the strongest responses within 100–200 μm of the soma) from synaptic responses. (E) A map of traces acquired at 12 adjacent stimulation positions spanning a 400 by 300 μm region in layer 2/3; this is an excerpt of the map pattern shown in (B).

Figure 6

The pulseEditor program for creating and saving standard stimulation pulses. (A) User controls for defining pulse parameters (number of pulses in the train, inter-pulse interval, pulse duration, pulse amplitude, initial delay), grouping pulses into an ordered sequence, and plotting the stimulus amplitude vs. time. (B) Example of stimulation waveform created using the pulseEditor user interface with parameters set as in panel A. Here the “additive” feature is used to combine a single positive pulse with a previously created multi-pulse waveform. (C) Custom “chirp” waveform created using the signalObject Matlab object; the frequency of the sinusoid increases linearly with time.

Figure 7

Ephus configuration for in vivo experiment. (A) Using the acquirer program several input channels can be configured for recording, triggered by an event. (B) Example of parameters simultaneously recorded during a behavioral experiment.

Figure 8

Schematic diagram describing connections and layered architecture for a selected set of software and hardware components of the core Ephus data acquisition system.

Figure 9

Sequence diagram of the propagation of events and the flow of control in response to user action. In this example, a user initiates an LSPS map by mouse-click in the mapper, and a number of programs, classes, user functions, toolboxes and device drivers interact to complete the map pixel-by-pixel.