Biology 450 - Animal Physiology Lab Fall 2007

Lab 1 - Introduction to Data Acquisition and Analysis

Most modern physiology laboratories use computer-based techniques for both data acquisition (usually abbreviated DAQ) and data analysis (sometimes abbreviated DAN).  Data acquisition involves both hardware and software, while analysis just uses software.  This week’s exercise is intended to familiarize you with the use of a typical DAQ/DAN system.

Background

Hardware

There are several steps involved in computer-based data acquisition – generating a signal, conditioning the signal (if necessary) and capturing the signal. This section briefly describes the components involved in this process.

Signal generation

Any data to be gathered by a DAQ system must ultimately appear in the form of a voltage. Sometimes the physiological variable of interest is already a voltage (e.g., membrane potential, electrocardiogram) and can be measured directly.  Otherwise, the variable must somehow be used to generate a voltage, the magnitude of which relates to the value of the variable. Devices that convert physical or chemical phenomena into electrical signals are commonly known as transducers.  A common example of a transducer is a microphone, which converts sounds waves (= pressure variations) into voltage signals.

There are two general kinds of transducers.  A passive transducer is one that generates voltage directly; for example, piezoelectric transducers produce a voltage when strained.  An active transducer is one that requires an electrical input in order to produce a voltage signal.  These transducers typically involve some sort of resistor as the primary sensor; a common example is a thermistor, a device whose resistance changes with temperature.  Both passive and active transducers will be used in this course.

Signal conditioning

Once a voltage signal has been generated, there is often a need for some sort of conditioning to help make the signal easier to record or interpret.  One problem with many signals from biological systems or some classes of transducers is that the voltages generated are very low.  In such cases, an amplifier must be used to boost the signal strength (amplification is also known as gain).  In addition, there may be perturbations, or noise, in the signal as the result of other electrical activity in the area.  For example, the electrical current in fluorescent lights and other devices may create an extraneous 60 Hz wave in a voltage signal if wires are not well shielded.  In such cases, a filter that removes noise at particular wavelengths may be helpful.  Many amplifiers include filtering capabilities.

In this course, we will be using two types of amplifiers.  Both can be used for basic amplification, but the two types differ in their additional capabilities:

Signal capture

PowerLab 425

PowerLab 425

Finally, the voltage signal must be read or recorded in some way.  Most simply, a voltmeter or mechanical chart recorder can be used for this purpose, but nowadays the more common solution is to use an analog-to-digital converter (abbreviated A/D or ADC) to transfer the data to a computer.  An A/D board translates (analog) voltages into (digital) numbers that are typically passed to software that presents these values in some useful formats and records them to disk if desired.  Most A/D boards can receive more than one signal at a time (multi-channel capability). Better A/D boards will have built-in conditioning abilities, such as amplification and filtering, and have voltage output channels controlled by software.

Our A/D system is the PowerLab 425.  It provides four input channels, one output channel, signal gain and some basic filtering capabilities.

Software

Chart Sample Screen

Software-based Chart Recorder

Most DAQ/DAN software is designed to look and function much like its older counterparts, the paper-based chart recorder and the oscilloscope.  However, these programs also have capabilities well beyond these earlier methods of data capture.

In general, data acquisition involves setting hardware and software values such that a strong signal is present on each channel.  Gains, offsets, filters and sampling rates may all have to be adjusted to achieve this.  Some channels may be set up to convert signals from raw voltages into the units of interest (e.g. mmHg, °C), or to extract useful values from data recorded on another channel (e.g. a running average or a pulse rate). Data recordings are usually easy to start, stop, and save.  Most programs allow you to make notations as you record, to indicate what was occurring at particular times.

Once data are recorded, they can typically be further manipulated or analyzed to determine statistics such as mean, maximum and minimum values during a given time.  You can also export data for import into a spreadsheet or statistical package.

Exercises

These exercises will introduce you to the software and hardware for the course, generally following the reverse order of the presentation above.

Software – Chart

We will use two DAQ/DAN programs in this course. Chart, which acts like a chart recorder, can record voltage inputs for an indefinite period, but is not well suited to recording very rapid events. Scope, which acts like an oscilloscope, is best used for recording fast, short lived events

Introduction to Chart

To get familiar with Chart, we will use a file containing some sample data.

Procedure:

  1. To start Chart, find the shortcut on the Windows desktop.
  2. The “Experiments Galley” window should appear when Chart starts. If it does not, choose “File…Experiments Gallery.” Then find the file “Waveforms.adicht” and open it.
  3. Use this file to follow the tutorial provided by the instructor in lab.

Recording and analyzing input

In this exercise, you will set up Chart to record pulse pressure traces provided by a fingertip pressure transducer.

Procedures:

Initial setup
  1. Set up two channels for recording - that is, eliminate all but two channels from the display - by using “Setup...Channel settings.” The number of channels setting is set in the lower left of the window.
  2. Verify that the range for Channel 1 is set to the default value of 10V and the recording rate is set to 1k/s in Chart.
  3. Pulse transducer

  4. Connect the pulse transducer to Input 1 of the PowerLab using the BNC connector, and strap the other end around the fingertip of a member of your lab group.
  5. Begin recording - the signal on Channel 1 should show a fairly flat line at about 0.0V.
Adjusting settings

Why does the line appear flat, or nearly so? The transducer is a passive one (that is, it produces a voltage by itself), but generates only a few hundred millivolts. The settings need to be changed to better suit this transducer.

The components of the Chart window

  1. First find a suitable voltage range. Use the Range/Amplitude pop-up menu at the upper right to set the value to 200 mV; the pulse signal should be much easier to see when you start recording again. If there’s still a lot of empty screen above and below the trace, try decreasing the range further. If the trace is going off the edge of the display, increase the range until it fits.
  2. Once the correct voltage range is selected, you can use the Scale pop-up menu or Scaling buttons to fine-tune the relative amplitude of the trace. Important: Do not use the scaling feature as a substitute for finding an appropriate voltage range!
  3. The choice of recording speed is a little more flexible, but the current speed of 1000 samples per second is more than needed for an event that occurs about once a second or so. Use the compression buttons at the lower right to set the display at 1:1 (that is, uncompressed). You’ll see that the pressure trace is very spread out, meaning a slower recording speed would still capture all the detail needed.
  4. Using the Rate/Time pop-up menu in the upper right, try a few different recording speeds slower than 1k/s to see which still give acceptable traces. When the shape of the pressure trace begins to degrade, recording is too slow.
Comments

It can be useful to insert comments as you record data to identify experiments or treatments, explain unusual values, etc.

  1. To add a comment at any time as a file is being recorded in Chart, simply start typing. Your text will appear just below the toolbar. When done, hit Enter; the comment appears as a line on the main chart area with the text visible along it. Try entering a comment at some point while recording.
  2. You can view all your comments by selecting “Window...Comments” from the main menu.
  3. You can also use the “Window...Notebook” menu item to access a text page associated with the Chart file as a whole. This is a useful place to put general information about the recordings.
Basic analysis

Recorded data is often not especially useful it its raw form. Instead, some type of analysis is needed to provide information on rates of change, maximum or minimum values, event durations, etc. In the case of the trace you just recorded, the interest is not in the pressure at any given time, but in the heartbeat frequency or pulse rate.

  1. One general technique available in Chart to measure changes in signal strength or in time is the Marker tool. The Marker looks like an M with a triangle under it and has its “home” in the lower left of the Chart window.
  2. To determine pulse rate, drag this tool to one of the peaks of the pressure trace. The Rate/Time and Range/Amplitude displays will change from an absolute readout to a differential (or delta) readout
  3. Move the cursor to another peak to determine the change in time between peaks. The inverse of this value will be the pulse rate. (Note: any measurement like this involves some amount of error. The relative magnitude of this error can be reduced by measuring the time taken for multiple heartbeats rather than just one.)
  4. If you lose track of the Marker, click on its home and it will reappear there.
  5. Chart can also calculate event frequencies directly. In the pop-up menu for Channel 2, choose “Cyclical measurements.” The window that appears allows you to determine the frequency of events that exceed a threshold voltage. Although settings can be changed manually, many useful presets are available. In the lower left of the window, choose “Cardiovascular - Finger Pulse” from the pop-up list (many other settings will also work) and click “OK.”
  6. You should see the pulse rate of your last recording displayed on the lower trace. The calculated rate usually varies slightly over time.
  7. To turn this function back off, select “No calculation” from the pop-up menu for Channel 2.
  8. Answer question 1 on the worksheet.

Creating stimuli

In this exercise, you will practice creating output signals such as those we will use to stimulate various physiological events. In order to verify that the output you generate has the intended pattern, you will send each stimulus back into one of the input channels so you can see each signal.

Procedure:

  1. Use a BNC cable to connect the Powerlab’s positive (+) Output channel to the Input 1 channel on the same box.
  2. Set the range for Input 1 to 10V.
  3. Record long enough to verify that the output is currently at 0.0V.
  4. From the menu choose “Setup...Stimulator.”
  5. In the Stimulator setup window:
  6. Leave the Stimulator Setup window open and start recording. The Stimulate button should become active.
  7. Click the Stimulate button to start the stimuli. You should see the expected pattern (0.5s of 5.0V followed by 0.5s of 0.0V) in the Channel 1 trace. Because “Continuously” was chosen, the stimuli will continue until the “Off” button is pressed.

More typically in this lab, you will need to send out just one or a few brief stimuli.

  1. Make these changes to the Stimulator setup window:
  2. Start recording and click “Stimulate.” You should see a single, short stimulus. If it does not appear, you may need to increase the recording speed.
  3. Because the Stimulator Setup window is fairly large, it can be easier to use the Stimulator Panel when recording. To see this, close the Stimulator Setup window and choose “Setup...Stimulator Panel” from the main menu. This panel allows you to change a few stimulus settings and to trigger the stimulus manually.

Hardware

Using the differential amplifier

Each lab station has a four channel differential amplifier, the DP-304.  Not all of the amp’s functions will be examined.

Procedure:

  1. Using the Stimulator control panel, set up a continuous waveform under manual control, with an output range of 200mV and amplitude of ~1mV, and a baseline of 0.000V.  Choose other settings as desired.
  2. With the Powerlab’s + Output channel connected directly to Input channel 1, verify your waveform settings as you did under Creating stimuli above .
  3. Turn the stimulator off (if currently on).
  4. Make sure the amplifier is turned on.
  5. For Channel 1 on the amplifier, set the gain to 100 and the DC Level to the middle of its range.  Make sure the Low Pass Filter knob is set to 10, the High Pass Filter knob to 0.1, and the Mode to DC. Finally, flip the switch for the “+” input to on and the “-” input to off.
  6. Now connect the Powerlab’s “+” Output channel to the Channel 1 “+” input of the amp.  Connect Output 1 of the amp to the Powerlab’s Input channel 1. 
  7. Start the stimulator.
  8. Note the recorded voltages relative to the voltage being generated by the stimulator.  Now adjust the gain and DC level and note the effects.

Using the bridge amplifier and sample transducers

In this exercise, you will use the ETH-400 bridge amp to power a “respiration” transducer (the “RM-100”).

Procedure:

  1. Make sure the bridge amp is plugged in.
  2. Connect the RM-100 to the back of the bridge amp, along with a BNC cable from the bridge amp output to the Powerlab’s Input channel 1.
  3. Try getting a signal from the RM-100 by breathing on the sensor tip.  Adjust the gain on the bridge amp and/or the voltage range in Chart to get a strong signal.
  4. Calculate your respiration rate using one of the techniques described for your pulse.
  5. Answer question 2 on the lab worksheet. You might want to verify your answer to 2b through some suitable tests.