Microcontroller Action Potential Generator

Here I demonstrate how to use a single microcontroller pin to generate action-potential-like waveforms. The output is similar my fully analog action potential generator circuit, but the waveform here is created in an entirely different way. A microcontroller is at the core of this project and determines when to fire action potentials. Taking advantage of the pseudo-random number generator (rand() in AVR-GCC’s stdlib.h), I am able to easily produce unevenly-spaced action potentials which more accurately reflect those observed in nature. This circuit has a potentiometer to adjust the action potential frequency (probability) and another to adjust the amount of overshoot (afterhyperpolarization, AHP). I created this project because I wanted to practice designing various types of action potential measurement circuits, so creating an action potential generating circuit was an obvious perquisite.

 

The core of this circuit is a capacitor which is charged and discharged by toggling a microcontroller pin between high, low, and high-Z states. In the high state (pin configured as output, clamped at 5V) the capacitor charges through a series resistor as the pin sources current. In the low state (pin configured as output, clamped at 0V) the capacitor discharges through a series resistor as the pin sinks current. In the high-Z / high impedance state (pin configured as an input and little current flows through it), the capacitor rests. By spending most of the time in high-Z then rapidly cycling through high/low states, triangular waveforms can be created with rapid rise/fall times. Amplifying this transient and applying a low-pass filter using a single operational amplifier stage of an LM-358 shapes this transient into something which resembles an action potential. Wikipedia has a section describing how to use an op-amp to design an active low-pass filter like the one used here.

The code to generate the digital waveform is very straightforward. I’m using PB4 to charge/discharge the capacitor, so the code which actually fires an action potential is as follows:

// rising part = charging the capacitor
DDRB|=(1<<PB4); // make output (low Z)
PORTB|=(1<<PB4); // make high (5v, source current)
_delay_ms(2); // 2ms rise time
	
// falling part
DDRB|=(1<<PB4); // make output (low Z)
PORTB&=~(1<<PB4); // make low (0V, sink current)
_delay_ms(2); // 2ms fall time
_delay_us(150); // extra fall time for AHP

// return to rest state
DDRB&=~(1<<PB4); // make input (high Z)

Programming the microcontroller was accomplished after it was soldered into the device using test clips attached to my ICSP (USBtinyISP). I only recently started using test clips, and for one-off projects like this it’s so much easier than adding header sockets or even wiring up header pins.

I am very pleased with how well this project turned out! I now have an easy way to make irregularly-spaced action potentials, and have a great starting point for future projects aimed at measuring action potential features using analog circuitry.

Project code (GitHub)

Notes

  • Action potential half-width (relating to the speed of the action potential) could be adjusted in software by reducing the time to charge and discharge the capacitor. A user control was not built in to the circuit shown here, however it would be very easy to allow a user to switch between regular and fast-spiking action potential waveforms.
  • I am happy that using the 1n4148 diode on the positive input of the op-amp works, but using two 100k resistors (forming a voltage divider floating around 2.5V) at the input and reducing the gain of this stage may have produced a more reliable result.
  • Action potential frequency (probability) is currently detected by sensing the analog voltage output by a rail-to-rail potentiometer. However, if you sensed a noisy line (simulating random excitatory and inhibitory synaptic input), you could easily make an integrate-and-fire model neuron which fires in response to excitatory input.
  • Discussion related to the nature of this “model neuron” with respect to other models (i.e., Hodgkin–Huxley) are on the previous post.
  • Something like this would make an interesting science fair project

     

Action Potential Generator Circuit

Few biological cells are as interesting to the electrical engineer as the neuron. Neurons are essentially capacitors (with a dielectric cell membrane separating conductive fluid on each side) with parallel charge pumps, leak currents, and nonlinear voltage-dependent currents. When massively parallelized, these individual functional electrical units yield complex behavior and underlie consciousness. The study of the electrical properties of neurons (neurophysiologically, a subset of electrophysiology) often involves the development and use of sensitive electrical equipment aimed at studying these small potentials produced by neurons and currents which travel through channels embedded in their membranes. It seems neurophysiology has gained an emerging interest from the hacker community, as evidenced by the success of Back Yard Brains, projects like the OpenEEG, and Hack-A-Day’s recent feature The Neuron – a Hacker’s Perspective.

In pondering designs for complex action potential detection and analysis circuitry, I realized that it would be beneficial to be able to generate action-potential-like waveforms on my workbench. The circuit I came up with to do this is a fully analog (technically mixed signal) action potential generator which produces lifelike action potentials.

 

Cellular Neurophysiology for Electrical Engineers (in 2 sentences): Neuron action potentials (self-propagating voltage-triggered depolarizations) in individual neurons are measured in scientific environments using single cell recording tools such as sharp microelectrodes and patch-clamp pipettes. Neurons typically rest around -70mV and when depolarized (typically by external excitatory input) above a threshold they engage in a self-propagating depolarization until they reach approximately +40mV, at which time a self-propagating repolarization occurs (often over-shooting the initial rest potential by several mV), then the cell slowly returns to the rest voltage so after about 50ms the neuron is prepared to fire another action potential. Impassioned budding electrophysiologists may enjoy further reading Active Behavior of the Cell Membrane and Introduction to Computational Neuroscience.

The circuit I describe here produces waveforms which visually mimic action potentials rather than serve to replicate the exact conductances real neurons employ to exhibit their complex behavior. It is worth noting that numerous scientists and engineers have designed more physiological electrical representations of neuronal circuitry using discrete components. In fact, the Hodgkin-Huxley model of the initiation and propagation of action potentials earned Alan Hodgkin and Andrew Huxley the Nobel Prize in Physiology and Medicine in 1936. Some resources on the internet describe how to design lifelike action potential generating circuits by mimicking the endogenous ionic conductances which underlie them, notably Analog and Digital Hardware Neural Models, Active Cell Model, and Neuromorphic Silicon Neuron Circuits. My goal for this project is to create waveforms which resemble action potentials, rather than waveforms which truly model them. I suspect it is highly unlikely I will earn a Nobel Prize for the work presented here.

The analog action potential simulator circuit I came up with creates a continuous series action potentials. This is achieved using a 555 timer (specifically the NE555) in an astable configuration to provide continuous square waves (about 6 Hz at about 50% duty). The rising edge of each square wave is isolated with a diode and used to charge a capacitor*. While the charge on the capacitor is above a certain voltage, an NPN transistor (the 2N3904) allows current to flow, amplifying this transient input current. The capacitor* discharges predictably (as an RC circuit) through a leak resistor. A large value leak resistor slows the discharge and allows that signal’s transistor to flow current for a longer duration. By having two signals (fast and slow) using RC circuits with different resistances (smaller and larger), the transistors are on for different durations (shorter and longer). By making the short pulse positive (using the NPN in common collector configuration) and the longer pulse negative (using the NPN in common emitter configuration), a resistor voltage divider can be designed to scale and combine these signals into an output waveform a few hundred mV in size with a 5V power supply. Pictured below is the output of this circuit realized on a breadboard. The blue trace is the output of the 555 timer.

*Between the capacitance of the rectification diode, input capacitance of the transistor, and stray parasitic capacitance from the physical construction of my wires and the rails on my breadboard, there is sufficient capacitance to accumulate charge which can be modified by changing the value of the leak resistor.

This circuit produces similar output when simulated. I’m using LTspice (free) to simulate this circuit. The circuit shown is identical to the one hand-drawn and built on the breadboard, with the exception that an additional 0.1 µF capacitor to ground is used on the output to smooth the signal. On the breadboard this capacitance-based low-pass filtering already exists due to the capacitive nature of the components, wires, and rails.

A few improvements naturally come to mind when considering this completed, functional circuit:

  • Action potential frequency: The resistor/capacitor network on the 555 timer determines the rate of square pulses which trigger action potentials. Changing these values will cause a different rate of action potential firing, but I haven’t attempted to push it too fast and suspect the result would not be stable is the capacitors are not given time to fully discharge before re-initiating subsequent action potentials.
  • Microcontroller-triggered action potentials: Since action potentials are triggered by any 5V rising edge signal, it is trivially easy to create action potentials from microcontrollers! You could create some very complex firing patterns, or even “reactive” firing patterns which respond to inputs. For example, add a TSL2561 I2C digital light sensor and you can have a light-to-frequency action potential generator!
  • Adjusting size and shape of action potentials: Since the waveform is the combination of two waveforms, you can really only adjust the duration (width) or amplitude (height) of each individual waveform, as well as the relative proportion of each used in creating the summation. Widths are adjusted by changing the leak resistor on the base of each transistor, or by adding additional capacitance. Amplitude and the ratio of each signal may be adjusted by changing the ratio of resistors on the output resistor divider.
  • Producing -70 mV (physiological) output: The current output is electirically decoupled (through a series capacitor) so it can float at whatever voltage you bias it to. Therefore, it is easy to “pull” in either direction. Adding a 10k potentiometer to bias the output is an easy way to let you set the voltage. A second potentiometer gating the magnitude of the output signal will let you adjust the height of the output waveform as desired.
  • The 555 could be replaced by an inverted ramp (sawtooth): An inverted ramp / sawtooth pattern which produces rapid 5V rising edges would drive this circuit equally well. A fully analog ramp generator circuit can be realized with 3 transistors: essentially a constant current capacitor charger with a threshold-detecting PNP/NPN discharge component.
  • This action potential is not all-or-nothing: In real life, small excitatory inputs which fail to reach the action potential threshold do not produce an action potential voltage waveform. This circuit uses 5V rising edges to produce action potential waveforms. However, feeding a 1V rising edge would produce an action potential 1/5 the size. This is not a physiological effect. However, it is unlikely (if not impossible) for many digital signal sources (i.e., common microcontrollers) to output anything other than sharp rising edge square waves of fixed voltages, so this is not a concern for my application.
  • Random action potentials: When pondering how to create randomly timed action potentials, the issue of how to generate random numbers arises. This is surprisingly difficult, especially in embedded devices. If a microcontroller is already being used, consider Make’s write-up on the subject, and I think personally I would go with a transistor-based avalanche nosie generator to create the randomness.
  • A major limitation is that irregularly spaced action potentials have slightly different amplitudes. I found this out the next day when I created a hardware random number generator (yes, that happened) to cause it to fire regularly, missing approximately half of the action potentials. When this happens, breaks in time result in a larger subsequent action potential. There are several ways to get around this, but it’s worth noting that the circuit shown here is best operated around 6 Hz with only continuous regularly-spaced action potentials.

In the video I also demonstrate how to record the output of this circuit using a high-speed (44.1 kHz) 16-bit analog-to-digital converter you already have (the microphone input of your sound card). I won’t go into all the details here, but below is the code to read data from a WAV file and plot it as if it were a real neuron. The graph below is an actual recording of the circuit described here using the microphone jack of my sound card.

import numpy as np
import matplotlib.pyplot as plt
Ys = np.memmap("recording.wav", dtype='h', mode='r')[1000:40000]
Ys = np.array(Ys)/max(Ys)*150-70
Xs = np.arange(len(Ys))/44100*1000
plt.figure(figsize=(6,3))
plt.grid(alpha=.5,ls=':')
plt.plot(Xs,Ys)
plt.margins(0,.1)
plt.title("Action Potential Circuit Output")
plt.ylabel("potential (mV)")
plt.xlabel("time (ms)")
plt.tight_layout()
plt.savefig("graph.png")
#plt.show()

Let’s make some noise! Just to see what it would look like, I created a circuit to generate slowly drifting random noise. I found this was a non-trivial task to achieve in hardware. Most noise generation circuits create random signals on the RF scale (white noise) which when low-pass filtered rapidly approach zero. I wanted something which would slowly drift up and down on a time scale of seconds. I achieved this by creating 4-bit pseudo-random numbers with a shift register (74HC595) clocked at a relatively slow speed (about 200 Hz) having essentially random values on its input. I used a 74HC14 inverting buffer (with Schmidt trigger inputs) to create the low frequency clock signal (about 200 Hz) and an extremely fast and intentionally unstable square wave (about 30 MHz) which was sampled by the shift register to generate the “random” data. The schematic illustrates these points, but note that I accidentally labeled the 74HC14 as a 74HC240. While also an inverting buffer the 74HC240 will not serve as a good RC oscillator buffer because it does not have Schmidt trigger inputs.

The addition of noise was a success, from an electrical and technical sense. It isn’t particularly physiological. Neurons would fire differently based on their resting membrane potential, and the peaks of action potential should all be about the same height regardless of the resting potential. However if one were performing an electrical recording through a patch-clamp pipette in perforated patch configuration (with high resistance between the electrode and the internal of the cell), a sharp microelectrode (with high resistance due to the small size of the tip opening), or were using electrical equipment or physical equipment with amplifier limitations, one could imagine that capacitance in the recording system would overcome the rapid swings in cellular potential and result in “noisy” recordings similar to those pictured above. They’re not physiological, but perhaps they’re a good electrical model of what it’s like trying to measure a physiological voltage in a messy and difficult to control experimental environment.

This project was an interesting exercise in analog land, and is completed sufficiently to allow me to move toward my initial goal: creating advanced action potential detection and measurement circuitry. There are many tweaks which may improve this circuit, but as it is good enough for my needs I am happy to leave it right where it is. If you decide to build a similar circuit (or a vastly different circuit to serve a similar purpose), send me an email! I’d love to see what you came up with.

 

UPDATE: add a microcontroller

I enhanced this project by creating a microcontroller controlled action potential generator. That article is here: https://www.swharden.com/wp/2017-08-20-microcontroller-action-potential-generator/


     

TTL Triggered Stimulus Generator

I was presented with a need to rapidly develop a pulse generator to take a TTL input and output a programmable output (for now 0.1 ms pulses at 20 Hz for as long as the input is high). I achieved this with a one-afternoon turnaround and the result looks great! This post documents the design and fabrication of this prototype device, with emphasis placed on design considerations and construction technique. It is also worth noting that by stocking large quantities of frequently-used items, inventors can build beautiful and functional prototypes for new ideas at the drop of a hat. While it’s easy to inexpensively accumulate tens of thousands of passive components (resistors, capacitors, etc.), it’s the slightly more expensive components that people tend to order only when they need it for a project. However, paying high shipping rates or waiting months for items to arrive from overseas dramatically increases the barrier for initiating new projects. In my own workshop I have noticed that stocking large volumes of slightly more costly items (inductors, microcontrollers, connectors, enclosures, LED bezels, etc.) lowers the barrier for me to start new projects, and has proved to be a good investment! Now I can build a product on the same day that I have the idea! Today’s idea takes the form of a TTL-controlled pulse generator for physiology applications.

I designed the enclosure before I designed the circuit. Metal enclosures are always expensive compared to their plastic counterparts. Steel enclosures are difficult to drill, and aluminum enclosures are expensive. My most cringe-worthy stocking expenditure is ordering metal enclosures in quantities of 10+. The last I checked this specific one is listed as, “Aluminum Instrument Box Enclosure Case+Screw For Project Electronic 26X71X110MM” and is a little under $4 each. Brass hex stand-off nuts and black steel screws don’t exactly match the aluminum, but they’re what I had on hand. I knew I would need power and a BNC input and output, so I put those 3 on the back. I wasn’t sure about the exact functionality of this device (and it may change after it is initially implemented) but I thought a single button and two LEDs would be a good starting point.

The circuit demonstrates the general flow of this device: a microcontroller-controlled project with a buffered output. I drew this schematic after I finished the build (I kept adding passives here and there as I tested it out) but before I started I knew the gist of how I would organize the project. Mentally I knew that as long as my microcontroller (ATTiny2313) could sense the TTL input and had control over all outputs (LEDs and BNC alike), I had a lot of flexibility to control the operation of this device in software. I used a generic LM7805 linear voltage regulator with a few decoupling capacitors to take a who-knows-what input voltage (up to 40V) and turn it into a stable 5V output. Note that both inputs (the BNC TTL input and the push-button) have decoupling capacitors near the microcontroller input pin to aid in debouncing.

I’m leaning on a 74HC541 inverting line driver to clamp the output voltage firmly at TTL levels. The microcontroller (an ATTiny2313) isn’t really designed to source of sink much current (I think it’s rated to 20 mA max) and I don’t know about the input circuitry of the stimulus isolator I intend to control (and don’t forget about the impedance of 50-ohm cable). The line driver helps me take some of the pressure off the microcontroller and help me feel better about reliably driving the output BNC.

Should I have optically isolated the input? Well, probably not… the application at hand is low importance. If I wanted to rely on optical isolation I would probably lean on the H11B1 as previously used in my opto-isolated laser build. In retrospect I kind of wish I had just because it would have been cooler!

I added a header to allow me to program the microcontroller with a programmer configured with test clip grabbers. I have an AVR ISP MKII (clone), and building a programming adapter that uses test clips was one of the best decisions I ever made! It makes programming (and the inevitable re-programming) a breeze.

The program isn’t too complex. It uses a polling method to continuously check for the state of the input TTL. When it’s high, it starts a new cycle (0.1 ms pulse, 49.9ms delay, yielding 20 Hz). The code is ready to add a “mode select” feature (which uses the front-panel push-button to select different stimulation protocols), but that functionality is not included in the example below. Note that a lot of the millisecond and microsecond delays are empirically determined by picking a value and checking its output on the oscilloscope. I should note that absolute timing isn’t critical for my application, as long as it’s consistent. For this reason I’m not relying on the internal RC clock (which is temperature sensitive), but instead am using an external 20MHz crystal as a time source. It’s still temperature sensitive (and so are the loading capacitors on each side of it), but dramatically less so than the RC option. Note that the crystal wasn’t in the original photos, but it was added for later photos.

Configure the ATTiny2313 to use an external crystal clock source

@echo off
avrdude -c usbtiny -p t2313 -U lfuse:w:0xff:m -U hfuse:w:0xdf:m -U efuse:w:0xff:m
pause

The core program (main.c)

#define F_CPU 20000000UL
#include <avr/io.h>
#include <util/delay.h>

volatile char state=0;

void output_HIGH(){PORTB|=(1<<PB4);}
void output_LOW(){PORTB&=~(1<<PB4);}
void LED1_ON(){PORTB|=(1<<PB3);}
void LED1_OFF(){PORTB&=~(1<<PB3);}
void LED2_ON(){PORTB|=(1<<PB2);}
void LED2_OFF(){PORTB&=~(1<<PB2);}

void singlePulse_20Hz_100us(){
	output_HIGH();
	_delay_us(100);
	output_LOW();
	_delay_us(900);
	LED2_ON();
	_delay_ms(20);
	LED2_OFF();
	_delay_ms(28);
	_delay_us(920);
}

void poll(){
	if ((PIND&(1<<PD4))){singlePulse_20Hz_100us();}
}

int main(void){
	DDRB=255; // all outputs
	DDRD=0; // all inputs
	PORTD=(1<<PD5); // pull front button high
	LED1_ON();
	for(;;){
		poll();
	}
}

Compile “main” and load it onto the ATTiny2313

@echo off
del *.elf
del *.hex
avr-gcc -mmcu=attiny2313 -Wall -Os -o main.elf main.c -w
avr-objcopy -j .text -j .data -O ihex main.elf main.hex
pause
avrdude -c usbtiny -p t2313 -U flash:w:"main.hex":a 

I didn’t think to check my height profile! I got lucky, and things fit fine. Socketed ICs can be close calls, and so can vertically-installed electrolytic capacitors. Now that it was programmed and everything fit, it was time to seal it up and make labels.

The finished product looks great! Never underestimate the power of clear labels and square outlines. Following deployment, a couple screws will let me open it up and access the programming header in case I need to change the stimulation protocols stored in the microchip. I am pleased with how professional of a result I was able to achieve in one sitting! I look forward to seeing how this device works for my application.

PS: Microcontroller code for this project (and many others) is stored in my ever-growing AVR-Projects GitHub page: https://github.com/swharden/AVR-projects

PPS: I smiled when a Google search revealed the PulsePal, “A low-cost programmable pulse generator for physiology and behavior”.