Spinal Cord Research Centre







SCRC Data Capture and Analysis Software Fact Sheet

[ Features | Our Software | System Requirements & Options | Contact | Suppliers: PowerDAQ (notes), NI-DAQ, Linux ]

Features


Our data capture and analysis software is available for Pentium-class PCs running the Linux operating system, offering a number of compelling features.

  • Low system cost: a complete Pentium-based data capture and analysis system can be put together for under $11,500 Canadian (plus taxes). This includes the $7000 license fee for our software, $3300 for the UEI PowerDAQ A/D converter and patch panel, and almost $1200 for the computer. The Linux operating system software, and the PowerDAQ device driver, are both available for free.
  • High performance: a 2 GHz PCI-bus Pentium system can sustain captures of 16 channels at over 20,000 KHz, storing all data to disk.
  • Industry-standard technology: because your system will be based on an industry-standard Intel Pentium PC, upgrades will be easily affordable and available.
  • Easy setup: a new channel monitor program lets you preview the signals, as well as signal levels, on all the channels you've chosen for capture. This can be a big help when setting amplifier gains before capturing. Also, current Red Hat Linux systems are much easier to install than QNX, older Linux, or most other UNIX-like systems.
  • Flexibility: your Linux system will come with the X Window system. You can run several applications at once and quickly switch between them. You can also take advantage of the rich set of free applications available for Linux systems.
  • Versatility: your PC can be configured as a dual-boot system. When not capturing or analysing under Linux, you can reboot into Windows to run other applications. Your PC does not need to sit idle when not capturing or analysing data - it is a fully functional PC which you can use to run your favorite software. Linux can write files to your Windows partition, so you can transfer all the plot files you produce during your analysis, then bring up Windows and import the plot files into any program that supports HPGL files (e.g. CorelDRAW). While analysing under Linux, you can also plot out directly to any printer supported by Linux's "magic filter" print tool.

About our software


Our software package includes several programs to aid in the capture and analysis of electrophysiological data. Unlike many data capture and analysis systems, these programs are specifically designed to meet the needs of neuroscience laboratories.

  • Calibrate: the calibrate program allows you to collect calibration information for the signals you capture, and display data using real-world units and names of your choice. This also enables the software to compensate for voltage changes introduced by amplifiers and filters that condition a signal before capture. The chanmon program allows you to monitor signal levels on all channels prior to data capture, to check for over- and under-range signals.
  • Cap: the cap program lets you set all the capture parameters (sampling rate, number of channels, run length, etc.), then handles the collection of "runs" of data from the A/D converter. The cap program can collect data on any channel as continuous waveforms, as triggered sweeps, or both. Parameters for data capture can be saved for quick reuse, in a menu and function key system. The cavg program can collect triggered sweeps and average them in real-time. Pre- and post-trigger capture is supported in both cap and cavg.
  • Analysis: the analysis program can perform over 50 basic types of analysis of the captured data, including examining raw data, averaging triggered sweeps sorted according to a number of criteria, obtaining triggered sweeps from continuous waveforms using a trigger of your choice & averaging these sweeps, a host of action-potential frequency analyses, action-potential cross-correlations and auto-correlations, burst duration and start/stop time analyses, and a number of X-Y plots of signal level. Many analyses break data down into cycles, to facilitate analysis of rhythmic events such as locomotion. Averages and correlations can be calculated with respect to either the amplitude of another waveform (e.g. membrane potential) or the time from the occurrence of an event (e.g. the end of flexor activity). Averaged sweeps can be stored as a "run" for later use by analysis or by any of the other programs in the package. All parameters for analysis can also be saved for later reuse. The analysis program can also perform high- or low-pass filtering, and/or full-wave rectification of continuous waveforms, and differentiation.
  • Qm: the qm program is used to obtain quick voltage and time measurements from triggered sweeps. Cursors can be placed on the sweeps to compare timing of events from different signal sources.
  • Many more: the frmsel program allows frames of data (triggered sweeps) to be previewed, and selected or deleted, or "tagged" into various categories. the raster program can produce 3-D "waterfall" plots of triggered sweeps; the peel program performs exponential peeling on the decay of a pulse; the isopot program produces isopotential contour maps from a matrix of voltage measurements; and the layout program allows you to put together final figures from plot files produced by the other programs. There are also several other programs geared to management of run files, conversion of other formats into run files, conversion of HPGL plot files to other formats, and printer/plotter support.

System Requirements


For the PC to support our software, just about any current generation hardware will do. Here are our recommendations:

  • 1.5 GHz or faster CPU,
  • Compatible Motherboard (with Intel chipset for Intel processor, or AMD chipset for AMD processor; ASUS motherboards have been a good bet)
  • 1 GB or more RAM (2-4 GB recommended),
  • 100 GB or larger hard drive (250-500 GB SATA recommended)
  • Logitech 3-button mouse or Intellimouse-compatible scroll mouse,
  • video adapter with at least 8 MB RAM (ATI or Intel chipsets preferred),
  • good quality 20" or larger monitor,
  • PCI-based Ethernet card or on-board Ethernet adapter,
  • brand-name CD or DVD Writer (8x or faster write speed, at least 2 MB write buffer),
  • United Electronics Industries PCI-based PowerDAQ A/D board
    or National Instruments M-series PCI-based NI-DAQ multifunction board
    (requires a full-height PCI slot).

System Options


We offer several options for putting a complete system together.

  • Pre-configured system: You can order the components for your system and have them shipped to us. We will put together the system, install the operating system and all software. We can even install Windows on the same system if you want. We will send you detailed specifications of the hardware and system software you need to order, and recommend suppliers. We will notify you when we receive your equipment. Once the system is complete and tested, we'll ship it to you.
  • On-site installation: We can send someone to you to install the operating system and all required software on your PC, at your site. Any custom configurations can be handled in this way. We'll make sure that the system is configured to your specifications, and thoroughly test it on site. You will be charged for airfare and expenses for one person, for the duration of the installation.
  • Do-It-Yourself installation: If you want to tackle the entire installation yourself, we can coach you by e-mail or telephone on how to successfully install Red Hat Linux. We recommend you familiarize yourself with the installation of Red Hat Linux, by reading the installation instructions on their web site. The SCRC Data Capture and Analysis is available in an RPM (Red-Hat Package Manager) package, which is very easy to install once Red Hat Linux is up and running. We also make the UEI PowerDAQ driver for Linux available as an RPM package for ease of installation. You will be responsible for purchasing all hardware components, putting the system together, installing the Red Hat Linux system, and configuring the X Window System for operation with your graphics card.
  • Additional analysis workstation: For a license fee of $500 per system, you can use our software on additional PCs to set up analysis-only workstations. The data capture portion of the software will not be functional on these systems, but everything else is included. Analysis-only workstations can be set up to run under any version of Red Hat Linux, but 8.0 or 9 are recommended. Additional Linux systems can be set up as any of the above system options. The analysis software is now also available for Mac OS X, and runs under the Mac's X11 software package.

Tell us what sort of systems you want us to put together for you, and we'll quote you a price.

Who to contact


For further information, or to request a quotation, please contact us at the address, phone or FAX number, or e-mail address below:

Spinal Cord Research Centre
University of Manitoba
745 Bannatyne Ave., BMSB 409
Winnipeg, MB R3E 0J9 Canada

Phone: 204-789-3770
FAX: 204-789-3934

E-Mail: info@scrc.umanitoba.ca

 

 

Recommended Suppliers


UEI PowerDAQ A/D Converter Board

These are the recommended components to order from United Electronics Industries (UEI):

PD2-MF-16-3M/12H     16SE/8DI A/D, gains: 1,2,4,8; Two 12-bit D/As; 3 counter/timers; 32 digital I/O
(this card is UEI's replacement for the PD2-MF-16-1M/12H card which we've been using)
PD-BNC-16-KIT Complete kit: Includes PD-BNC-16, PD-CBL-96, PD-CBL-37 (this is a BNC patch panel and cables for the A/D)

You can get more information about these, including how to order, from their web site, http://www.ueidaq.com/. Contact UEI for the distributor in your country or region. The prices are approximately $1650 US for the A/D board and $400 US for the patch panel.

United Electronic Industries, Inc.
611 Neponset St.
Canton, MA 02021 USA
Ph.: 781-821-2890, FAX: 781-821-2891, Web: http://www.ueidaq.com/

Note: We've noticed that when we connect equipment directly to the PowerDAQ A/D card, via a patch panel, we sometimes experience sequential-channel crosstalk. This happens at very high channel scanning frequencies, when we use equipment that does not have a very low input impedance. In these situations, we had found it helpful to add UEI's PD-BUFF input amplifier to condition the signals and present a low impedance to the A/D inputs. This is not needed if all your signal sources already have very low-impedance (10 ohms or less), or if you don't exceed a channel scanning frequency of about 500 KHz. As UEI has now discontinued this amplifier, we recommend that you set the scanning frequency to 500000 or lower if you have any signal sources with an output impedance of over 10 ohms.

You may opt to build your own patch panel, instead of buying UEI's kit. See the UEI web site for other PowerDAQ accessories that are available for any custom solution you want to put together. We have written some instructions for builing a PowerDAQ patch panel and buffer amplifier enclosure.

We also recommend purchasing the PD-16K-FIFO upgrade for PowerDAQ A/D cards that have less than 16K of FIFO, as it greatly enhances the reliability of data capture at high speeds, virtually eliminating the possibility of buffer overruns. This is not a field upgrade, so it must be purchased when the A/D card is ordered. The new PD2-MF-16-3M/12H card has a 16K FIFO already, but most other PowerDAQ cards have only 1K.

National Instruments NI-DAQ multifunction A/D Converter Board

These are the recommended components to order from National Instruments:

NI PCI-6251     16SE/8DI A/D inputs, 16-bits, 1 MS/s
NI BNC-2090A shielded rack-mount BNC patch panel
NI SHC68-68-EPM shielded cable for M series, 2 m length

You can get more information about these, including how to order, from their web site, http://www.ni.com/. Contact NI for a distributor in your region. The prices are approximately $1100 US for the A/D board and $450 US for the patch panel.

National Instruments Corporation
11500 N Mopac Expwy
Austin, TX 78759-3504 USA
Ph.: 1-888-280-7645, FAX: 512-683-8411, Web: http://www.ni.com/

Red Hat Linux Operating System

Our software has been tested under the Red Hat Enterprise Linux (RHEL) 5 or 6 clones CentOS 5.0-5.9 & 6.0-6.4 and Scientific Linux 5.0-5.9 & 6.0-6.4, so that is the system we currently recommend. We've also tested it on Scientific Linux 4, a clone of Red Hat Enterprise Linux 4, so you shouldn't have any difficulty with RHEL4, SL4, or any other RHEL4 clone. Fedora 6 to 18 are also supported, though these have a shorter life-cycle than the RHEL releases.

Red Hat Enterprise Linux is purchased with a support contract from Red Hat. See http://www.redhat.com/ for details. Red Hat Enterprise Linux clones can be downloaded from the CentOS or Scientific Linux web sites, or one of their mirror sites. See http://www.centos.org/ or https://www.scientificlinux.org/ for details. Fedora Linux can be obtained from http://fedoraproject.org/wiki/ or one of its mirror sites.

Any Fedora OS older than Fedora 18 is no longer updated by the Fedora Project, so we don't recommend them for new installations. Red Hat Enterprise Linux 3 or older have not been tested, but will likely work, possibly requiring a recompiling of the source RPM package.

Support is now available for recent Ubuntu Linux distributions, 7.10 (Gutsy) and 8.04 (Hardy). Ubuntu 8.10 (Intrepid) and later have only been tested a little bit, but will likely work as well.

For more information, see our O/S requirements page.


See also: SCRC Software On-line Documentation




© Copyright 2013 G. R. Detillieux, Spinal Cord Research Centre, University of Manitoba. All Rights Reserved. Contact Us for more information.
Revised September 10, 2013.