Data Acqusition Software for Neurobiology using Matlab

Introduction

As part of an effort to make inexpensive and flexible biology lab instrumentation, we have written a Matlab program which:

• Simulates the function and appearance of a traditional oscilloscope and a pyhsiological stimulator.
• Accepts real input from either the Windows sound device or a National Instruments DAQ board.
• Produces real output from either the Windows sound device or a National Instruments DAQ board.
• Stores data in a format that other staff or student written analysis programs can use.

We used Matlab because it is a flexible programming language which includes the abilities to:

• generate graphic user interfaces (GUI).
• acquire data in realtime.
• provide extensive, easy to use analysis and plotting.

This page is divided into two parts; program use and program internal structure. Obviously, you don't need to understand the program internals to use it, as long as nothing goes wrong.

Using the Program

If you want to use the program you must have a licensed copy of Matlab release 14. Later in the fall we expect to have a version which will run standalone without Matlab. You then need to download the program we wrote (see links below). Be sure that your Matlab 'path' includes the folder where you stored the program. If you are not sure use the SetPath... option in the File menu to investigate. The NIDAQ version assumes that you have a National Instruments data aqusition card, and have installed the version 7.30 NIDAQ drivers. This program is cycle and memory hungry. It may not work well on slow machines. I have tested on

• The windsound device on a 866 MHz P3 with 256 Meg of memory. Program
• The NIDAQ device on a 3 GHz P4 with 1 Gbyte of memory. Program.
• Version by John Olthoff with better XL export function.

The GUI consists of two parts, a simulated oscilloscope and a simulated stimulator, hereafter refered to as the scope and stimulator.

The scope controls:

• Channel 1 and 2 can be turned off and on by clicking the check-boxes at the upper-right corner of the trace display. Each trace can be set to AC mode by clicking the check-boxes in the lower-right corner of the trace display. Traces may be positioned vertically by using the vertical sliders to the right of the display.
• Vertical voltage scale can be set from .001 to 10 volts full scale with the V fullscale control, for each channel separately. Channel 1 scale is shown on the y-axis of the plot. Channel 2 scale is shown in yellow at the top of the plot..
• Horizontal time scale can be set from .001 second to 30 seconds with the T fullscale control.
• Trigger source can be set to:
  • Manual, which activates the scope Trigger button. Pressing the Trigger button will cause the scope to acquire one trace. To quit from the program or change the scope time scale, the trigger mode must be Manual.
  • Continuous to acquire data as fast as possible.
  • External to cause the scope to acquire data when an external pulse is applied to analog input 2 with an amplitude greater than the value set in the Trigger Level control.
  • Channel-1 or Channel-2 which triggers the scope when the voltage on the respective channel is equal to the value set in the Trigger Level control.
• Sample rate (samples/second) can be set to 8000, 11000, 22000 or 44100 for the winsound device and to an arbitrary value for the NIDAQ device. Default is 10000 sample/sec.
• The Expand T control activates a cursor-based drag box. Click on the Expand T control, then click-drag-release in the scope trace display. The part of the waveform you dragged over will expand to fill the display in the horizontal direction. Voltage scaling is not affected. A scrollbar appears so that you can scroll through the entire waveform.
• Audio Ch1 and Ch2 play the traces through the sound card.
• The Measure control activates a cursor-based drag box. Click on the Measure control, then click in the scope trace display. The click sets a zero value. The difference between the zero value and current cursor position is placed in the edit fields below the control. Since each trace can have different gain, you must choose the trace. If you have an external amplifier between you experiment and the computer input, you can set the gain.
• Save stores the entire data structure of the scope on the disk using a standard dialog box.
• Restore reloads a saved data structure.
• exportXL saves the two voltage traces as an Excel datasheet, with time, trace1 and trace2 as columns.
• Export causes the entire data structure of the scope to appear in the standard Matlab workspace. You can then access any value from any control:
  • Volage traces are in variables ScopeData.y(:,1) and ScopeData.y(:,2) in units of volts.
  • Time base is in ScopeData.x in units of seconds.
  • Trigger level is in ScopeData.triggerlevel.
  • Sample rate is in ScopeData.Fsin.
  • To view the entire data structure type ScopeData(1) at the Matlab command prompt.
• Capture causes the scope traces to be copied to another window, time stamped, and formated for printing. Once a display has been captured, the standard Matlab print, export, save and edit commands may be used. For instance, you can add a title. Saving the captured image from the file menu allows you to repoen it at a later time. The image below was captured from the traces shown near the top of the page.

The stimulator controls.

• Trigger mode can be set to:
  • Single, which activates the Trigger button
  • Continuous to produce pulses at the rate specified by the Repeat Interval control when the Start button is pushed.
• The wavefrom can be set to single pulse, two pulse or tetanic. In tetanic mode, the trigger continuous mode is disabled.
• All pulse delays and durations are set with a set of edit fields and lef-right arrows. The stimulating waveform is drawn below the controls. The color of each time control corresponds to the color of a line on the drawing.
  
  • In one pulse mode you can set Delay 1 (trigger to pulse) and pulse duration.
  • In two pulse mode you can set Delay 1, Delay 2 (pulse to pulse) and pulse duration.
  • In tetanic mode you can set Delay 1, Delay 2 ( first pulse to train), Delay 3 (train to last pulse) and pulse duration. You can also set the tetanic duration which is the length of all the pulses in the train, and the interval which is the spacing of pulses within the train.
  • In all modes, you can set the repeat interval which determines how often the entire stimulus will be produced, if the trigger mode is set to continuous and the start button is pushed.
  • The following image shows the stimulator in tetanic mode. The length of each colored line on the drawing corresponds to the setting on the similar-colored control.
  • 
• Save stores the entire data structure of the stimulator on the disk using a standard dialog box.
• Export causes the entire data structure of the stimulator to appear in the standard Matlab workspace. You can then access any value from any control:
  • The stimulator waveform is in variable ScopeData.waveform
  • The delays are in ScopeData.delay1, ScopeData.delay2, ScopeData.delay3
  • The duration is in ScopeData.width.
  • Stimulus sample rate is in ScopeData.Fs.

   

Program Internal Organization

The program is structured as a Matlab function. Persistant data is stored in the UserData area of the figure. The initial execution of the function from the command line initializes a bunch of variables and the GUI, then exits. At that point, the GUI is drawn in the figure window and all the GUI controls are waiting patiently for a user action. Control returns to the main function under three conditions:

• The user triggers a GUI element, and hence a callback function. Each GUI element callback is defined by the following uicontrol parameter: 'CallBack',[data.myname,' action']. The structure element data.myname holds a string which is the name of the file holding the main function. The literal string which follows defines the actual action within the function.
  
• The DAQ toolbox timers are active and a timer event occurs (to acquire data or produce a pulse). The format for defining a timer action is: set(data.ai, 'TimerAction', {data.myname,'action'}). Where data.ai holds a handle to the analog input device, the litereral TimerAction specifies which action type will be defined and the cell-array {data.myname,'action'}specifies the function and parameter which will be occur when the DAQ timer times out..
  
• The DAQ toolbox trigger is active and a trigger event occurs (e.g. a voltage passes a threshold). The trigger actions are specified in a similar fashion to timer actions.

Each of the events or callbacks passes a string to the main function which is dispatched by a gigantic case statement to perform an action, perhaps modify the persistant data, then exit. Since the main function is not running most of the time, the Matlab command line stays active.

The DAQ toolbox provides an (almost) hardware-independent, abstract, data acqusition interface to Matlab. Several devices are supported. Currently separate versions of this program are written to support the Winsound device and National Instruments NIDAQ hardware. It turns out that there are some device dependencies. A flag must be set in the program to select the hardware to be used before you run it. The DAQ toolbox defines analog input and analog output objects which have quite complex, and potentially asynchronous, behavior. The usual get/set commands specify DAQ object parameters and read back their state. Debugging the porgram consisted mostly of figuring out how to set up DAQ objects and their parameters.

Note that it is possible to produce weird concurrent errors if the user happens to trigger a GUI element at just the wrong time. I am still working on this. There are a few sub-functions near the end of the program. One constructs the stimulator waveform. Another displays an scope trace.