Scientific Solutions ^® Inc.

LabMaster EP Software Suite

Scientific Solutions offers the Henry ElectroPhysiology Software Suite (The EP Suite). Developed for whole-cell recording and data analysis using the LabMaster, the EP Suite is an easy-to-use powerful graphical-based collection of programs and utilities designed for working ElectroPhysiologists.

The EP Suite provides the tools for designing and running voltage-clamp (and current-clamp) experiments, interactive communication with the Scientific Solutions LabMaster data acquisition hardware, efficient data-collection, run-time clamp monitoring and many analysis and data-editing tools.

The EP Suite Includes the following applications:

Henry
- The primary, clamp-control and data acquisition/analysis application
N-pro
- Noise Profiling and Filter tools for improving the Signal-to-Noise ratios of collected data
Vicar
- Virtual Chart Recorder
Pandora!
- Collection of analysis tools and utilities, I:V modeling, Histograms and Time analysis.

The EP Suite is designed from the ground-up to be a true multi-tasking 32-bit windows graphical program and takes full advantage of user friendly “point-and-click” and “drag-and-drop” facilities for designing voltage and current clamp protocols and for selecting data for analysis. A printed manual is not included, as the software provides on line context-sensitive help and most would agree that the software is intuitive and easy to use.

Software Requirements for the LabMaster PRO EP Software Suite:

Pentium II or better CPU with a PCI slot for installing the LabMaster PRO
icroSoft Windows 98 (2nd Edition), 2000, XP or Vista (32-bit version).

Please note:
The EP Software Suite is the result of many hours of work by highly talented researchers at the University of Glasgow. This project is ongoing, and like any advanced software product it is in constant flux - with things to do, changes to be made and new features to be incorporated. The applications and other modules comprising the EP Suite are designed to be intuitive and easy to use, subject to the constraints implied by the scientifically technical nature of the experimental conditions and electronic hardware in use.

The EP Suite is not yet released as commercial software. It is still being developed, and at this point is therefore provided at No Charge to our customers. This does not imply that it is a “light-weight” or “limited product.” On the contrary, it is a very complete and powerful set of tools and better than many high-priced commercial products currently in the market. At some point the software may be released as a commercial product for purchase. At this time we believe providing the software “free-of-charge” will allow users be able to cost effectively upgrade their systems and encourage more wide-spread use of the software which will help to make a better product. We encourage comments, suggestions and reports of problems. Your feedback will aid in the quick resolution of problems and help the ongoing development of the software suite.

Henry - The primary, clamp control and data acquisition and analysis application

A Protocol defines the way in which a particular voltage or current - clamp experiment is performed. The Henry EP Protocol Editor allows you to design your voltage-clamp or current-clamp experiment using an intuitive, graphical user interface (GUI), whereby clamp values, times, sampling parameters and digital output signals can be defined and changed using the computer mouse in a 'point-and-press' and 'drag-and-drop' system.
Once you have designed a Protocol using the Protocol Editor, you can run the experiment using the RUN command. The Protocol is then compiled into a binary 'event-list' which is loaded into the LabMaster driver and the appropriate clamp is turned on and set to the initial value for the first cycle. Then depending upon the Trigger Mode you are using, the Protocol either runs immediately or waits for either Keyboard or the appropriate Digital In signal before starting the run.
Data sets collected during the Protocol run are stored directly on disk in a 16-bit data format that includes information about the Protocol that was run, software version information for compatibility with future enhancements, Amplifier settings in effect when the data was collected, and the cell geometry settings when the data was collected.
The Henry application provides a variety of tools for analyzing the collected data including:
- I:V Analysis - Plotting of measured current versus voltage (I:V)
- I[ss]-I[i] Analysis - I:V curves for the Steady State I[ss] and Instantaneous I[i] currents and their differences using dynamic, dragable cursors to select the exact data point.
- Normalizing Data - View collected data from different cycles, which may have different 'Y' ranges, on the same, normalized scale, thus making it easier to spot kinetic (time scale) differences without the added complexity of magnitude differences.
- Time-of-Y Analysis - Allows you to create and display a curve connecting the times at which elicited currents from different cycles of the same Protocol reach a give fraction of their final (steady-state) values.
- Multi-File Analysis - This analysis consists of a series of similar files grouped together for common inspection, curve fitting and other analytical methods.
The Henry application includes tools for fitting a variety of curve types to raw data sets and some derived data. These are implemented, by default, using the well established, rapid and generally robust Levenberg-Marquadt function minimization algorithm, but you can choose to use the very much slower Direct Search method of Hooke and Jeeves, which may give better results in certain cases. Curve Fitting Includes:
- Current versus Time - Exponential rise, Sum of Exponents, Polynomials
- Current versus Voltage - Exponential rise, Sum of Exponents, Polynomials, Current (4-parameter), Conductance (3-parameter), GHK 'Open Channel'.
Data stored in Henry's Raw Data Files can be exported to a variety of file formats supported by common third-party data analysis/presentation programs.
- Tab-Delimited Plain Text (ASCII) - common format readable by word processing applications, spreadsheet programs and plotting programs such as Excel and Sigmaplot.
- Comma-Delimited format - similar to Tab, except data is separated by commas instead of the tab character. Again, very common open format.
- Data values exported are converted from the raw binary integers to their corresponding 'real' voltages and currents according to the LabMaster A/D Amplifier and Rig gains and offsets stored in the file.

N-Pro - An application for improving signal-to-noise ratios in data sets collected within the suite and with a wide variety of third-party software.

Noise Profiling Tool - A popular tool that has proved very useful for patch-clamp (single channel) data that allows you to inspect and remove noise of a cyclical or pseudo-cyclical nature (particularly that caused by AC mains supply).
Smoothing Techniques - Gaussian (or binomial smoothing) and Savitsky-Golay (Least-Squares filter).
Digital Filtering - Notch Filters, Band Pass, High Pass and Low Pass digital filters
FFT Analysis - Frequency Analysis using the Fast Fourier Transform
Wavelet Filtering - A good alternative to Noise Profiling when the underlying noise takes the form of a complex waveform.
LULU Filtering - Another good alternative to Noise Profiling when the data set is particularly 'spiky'. This is implemented as a preliminary tool in the current release.
Block-Median Pyramidal Transform Filtering - Under development in the current version.
N-Pro can work with files produced by a variety of third-party software packages, in their native formats, including:
- Zxon Binary Files - Axon Instruments' pClamp and other applications use this ABF format
- Bruxton Exchange Format - File format from Bruxton Corporation
- Cambridge File System - File format from Cambridge Electronic Designs (CED)
- HEKA Pulse and Pulse-Fit Files - Binary format from HEKA Electronik
- Whole Cell Patch Files - Format generated by WCP program from Strathclyde Electrophysiological Software.
- Henry's Raw Data Files - As expected, data files produced and/or edited with Henry are fully supported by all applications.
- Plain Text (ASCII) Files

Vicar - Virtual Chart Recorder allows you to monitor the input from a number of DC channels over long periods of time, without having to use a standard, paper-based device.

The application allows control of the LabMaster Analog Output channels and clamp control while recording a chart.
You have the ability to insert up to four predefined comments, or text at either the current point or a preceding point
Allows recording to continue while the Henry application is running a Protocol.

Pandora! - A collection of analysis tools and utilities for the analysis of single-channel (patch-clamp) data, as well as a variety of I:V modeling tools and conversion of 'third-party' data files into Henry's native format.

Please note that “Pandora!” is a developmental version as the software is not yet complete; it is ongoing, and many of the features are not fully functional. However, it is included in its present form as it is still helpful in many instances.

Current-Amplitude Histograms - Provides information on the number of different types of channels, or sub-conductance states of a single type, located within the patch.
Restoration Analysis - Attempts to recreate the 'ideal' current trace (without, baseline drift and other artifacts) to the location and duration of channel openings can be determined.
Dwell Time Analysis - Compilation of the time intervals for each channel opening (or closing) 'event' into histograms, for subsequent statistical analysis.
I:V Modeling Tools - One of the features of the Pandora! application is a collection of tools allowing you to create 'model' I:V curves using a variety of established (and experimental) algorithms.
- Amtmann-GHK I:V Models - This allows you to create steady-state I:V curves for three types of channels: inward rectifiers, outward rectifiers, and voltage independent - using the formula published by Anna Amtmann and Dale Sanders in 1999.
- GHK 'Open Channel' Models - This allows the creation of I:V curves using the classic Goldman-Hodgkin-Katz equation for a open channel, specifying its conductance and reversal potential.
Pandora! can work with files produced by a variety of third-party software packages, in their native formats, including:
- Axon Binary Files - Axon Instruments' pClamp and other applications use this ABF format
- Bruxton Exchange Format - File format from Bruxton Corporation
- Cambridge File System - File format from Cambridge Electronic Designs (CED).
- HEKA Pulse and Pulse-Fit Files - Binary format from HEKA Electronik.
- Whole Cell Patch Files - Format generated by WCP program from Strathclyde Electrophysiological Software.
- Henry's Raw Data Files - As expected, data files produced and/or edited with Henry are fully supported by all applications.
- Plain Text (ASCII) Files

Specifications subject to change without notice.