Synapse

This page introduces Synapse. It provides descriptions of how Synapse is used in electrophysiology and ion imaging.

Introduction

Synapse is a combined electrophysiology and ion imaging program running on a Macintosh or PPC. Synapse Image combines control, acquisition and analysis of both electrical signals and images in one program that uses the full bandwidth of a Macintosh computer. Synapse Image is a superset of Synapse.

The analog portion of Synapse is a full featured electrophysiology program which runs on a Macintosh or PPC computer. Synapse combines control, acquisition and analysis of both continuous and episodic data. Synapse analysis is automated by a macro language. Because the acquisition system may be controlled by the macro, it is possible to use Synapse in fully automated assays.

Synapse was conceived and developed in collaboration with Drs. Mark Mayer, James Russell, Phil Nelson and their colleagues at NIH. Support and design for Synapse also comes from universities and places as far away as Israel. Software was written by Jim Nash, Dr. Larry Woltz, Dawn Gregory and others at Synergy Research Inc.

Features

Simultaneous image and analog signal acquisition.
Acquire and analyze in the same program: assays.
Supports most electrophysiological techniques.
Control of recording and analysis from a Pascal-like programming environment.
Powerful, extensible analysis environment.
Algebraic scalar, signal and image calculator.
Motorized stage control
Dual wavelength ratio imaging.
User installable code resources.
Custom software development.
Source code available.

Areas of Research

Stationary Noise analysis
Single ion channel analysis
Fluorescence (ion) microscopy
Continuous D/A output from event file
8 channel analog - 2 channel video - digital control
Pharmacological basis of membrane currents and calcium concentration
Kinetics of drug induced currents
Learning
Cell growth
Temperature dependency of currents and calcium concentration
EPSC - ISH - PSTH - spike detection
Voltage clamp
Patch clamp

Example Applications

These short summaries show how Synapse facilitates research from acquistion to presentation. Protocols control drug application, image intensifier, shutters, clamp voltage. One acquires, reviews, categorizes, selects and then analyzes data using (user modifiable) analysis routines. Analysis produces tables of numbers and graphs that are exported to graphics and other analysis routines outside Synapse. One may copy data to a draw program or word processor.

Kinetics of membrane currents. Voltage steps and drugs are applied in the presence of other drugs. The response is fitted with multiple exponentials. The decay constants of many trials are written to a tabulated file and/or plotted. Here is shown a fitted curve with exponential manually extended beyond the fitting region.

Drug application at multiple holding potentials. Drugs are applied using hardware controlled through digital lines from the ITC-16. One run consists of multiple records (traces), each one having a different holding potential. The decay constants of multiple exponential functions are extracted from the curve during drug application or wash-out. The resulting data are saved in the form of a user defined table. Standard deviation and variance curves can be computed interactively.

Conditioning pulses with variable delay to a test pulse. A conditioning pulse of fixed or variable width is presented followed by a variable delay. Then a test pulse is presented yielding a family of curves having a decay component that is sensitive to the delay or variable pulse width. The curves are displayed, printed and selected for analysis. Time constants of multiple exponentials are saved in a table that are further analyzed by a statistical analysis program. Here is shown a diagram of the analog and digital outputs in a protocol having incrementing time.

Continuous data. Data are acquired to hard disk. Events are found, analyzed and/or converted to episodic data. Inter-event intervals are extracted and then plotted in a histogram or exported to a text file. This feature may be used for ISIH, PISH and single channel analysis.

Extraction of region of interest data from Fluorescence images. Images are acquired up to 15 frames per second in dual wavelength pairs. Calcium measurements are extracted and calcium images computed. Movies can be exported to image analysis programs as TIFF stacks.

Fluorescence image and photomultiplier data. Images are captured in Synapse in parallel with current, voltage and photomultiplier data. Regions of interest from fluorescence movies are converted to time varying signals. Current, voltage and PMT signals are carried forward in this reduction step. These data are viewed, selected and displayed as a raster display. Locations and integral of peaks are extracted. The raster display is cut from Synapse and pasted into a drawing program or word processing program for final publication. Raster data are exported in a format that can be read by a 3D graphics program for 3D display.

Stationary Noise. Noise is acquired before, during and after a drug application. The noise is transformed into power spectra that are averaged and then fitted with the sum of Lorentzians (1/f2).

Current - voltage curves. Macros can plot various x-y curves. I-V plots can be viewed (chord and slope conductance, leak subtracted) at the click of a button.

All point's histogram is used during acquisition to verify that the data is distributed reasonably. Histograms may be made of any measurement made in macros including amplitudes and elapsed time between events.

Specifications

Optional hardware and software

Analog and digital signals: ITC-16, Instrutech Corporation, Great Neck, NY
Image capture and digital control: LG-3, AG-5, Scion Corporation, Frederick, MD
Filter changer: Sutter Inst. Lambda-10 filter wheel, Metaltech, Vincent
Export analog to TAC (SKALAR), GW instruments, flat binary
Export images to NIH Image (freeware), IP Lab (Signal Analytics), TIFF, flat binary
Export analysis results in tab delimited ASCII supported by most analysis applications.
Import from Axon Instrument ABF format, flat files.

Analog/Digital system

Sample rate per channel 0.2 Hz to 200 KHz (5.0µs to 5.0s per sample).
Sample rate for 2 channels (example): 0.1 Hz to 100 KHz (10.0µs to 10.0s per sample).
Analog input channels 8, (see note 1 and 2).
Analog output channels 4 (one at a time).
Digital output lines 16 may be set and masked.
Digital input lines not used.
Note 1. All analog and digital signals are under control of Protocols and Macros. Note 2. All analog signals are calibrated in real world units.

Image system

Shutters controlled: 2
Filters controlled: 4 positions
Filter wheel speed: 8 speeds
Intensifier: via TTL lines
Frames per second 15 frames per second
Size and number of frames user configurable, limited by RAM or disk
Frame averaging (on board AG-5, on chip LG-3 (near future))

Analysis system

Trials may be categorized and/or collected in groups called operands.
Calculator window operates on real numbers and analog signals.
Macros operate on bytes, integers and reals; and on scalers, analog signals and images.
Extract macros, general macros and Log file algebraic calculator use Pascal.
Edit window available to modify Pascal macros.
Fast curve fitting includes simplex, conjugate gradient methods.
Curve fitting supports exponential, Lorentzian, 1/f, ion image calibration.
Display zoom, style, color, symbols, equal in time or sample, log-log, calibration bars, tics, grid.
Image regions of interest (ROI) have numerous flexible options.
On-line and off-line extraction of average from ROI.

Macintosh Computers

Mac II series, Centris, Quadra, Power PC (emulation), Powerbook.
System 7 required. Nu-bus required for hardware options. PCI bus available Winter 1996. Power PC native code available Spring 1996.

Documentation

Documentation is provided as Microsoft Word 6.0 files.

Learning Synapse takes you through the fundamentals of using Synapse.

Synapse User's Manual is an indispensible reference while designing protocols and analysis macros.

Synapse Image Extension Manual describes extensions to Synapse for the acquisition and analysis of images. It should be used with the Synapse User's Manual.

Synapse Release Notes accompany each release of Synapse. These are a companion to the User's Manuals.