February 06, 2014

Interpreting Rate Coding Data: Counting Spikes in a Tracing & Consequent Plotting of Firing Rate Versus Time

We acquire data by using the following device configuration (the green laptop cable will go to the laptop mic input, running on battery power) as shown below. Please see this link to learn about the anatomy of a coaxial cable, so that you can make a ground connection off a coaxial cable.

You can also take the ground off the reference point used for the Faraday cage clip, if you'd like. Incoming analog signals from the spikerbox will go into the internal ADC (Analog to Digital Converter) of the Conexant HD audio port of the laptop, whence the signal will be digitally processed. After a signal has been stored either in Audacity or in the BYB neuron recorder, we can open the'.aup' or the '.wav' file respectively later.

Here, I am attaching a typical wav file captured by striking the quadriceps tendon with a percussion hammer (knee jerk). This is a deep (tendon) reflex. I'll post more on this later. You need to open it using either of the two softwares listed. I am posting a screenshot on the right.
You can see three large spikes in the tracing. These spikes are actually not single/solitary, as they might innocuously suggest, but they are a conglomeration of many individual ones.

The below tutorial explains how to interpret these raw data.



By the way, there's no simple way to count spikes! First, we need to define spikes. We can fix an arbitrary threshold, beyond which we will label them as one. Here are some very rudimentary thoughts on counting:
  • Coupling/buffering the output from the laptop audio-out port via ICs like ULN 2004 Darlington transistor arrays to drive filament lamps [these filament lamps are a modest way to an integrator as the heat takes time to dissipate off]. The more the spike rates, greater will be the brightness. Then pick-up this optical signal by an LDR (Light Dependent Resistor) and then noting the resistance change [precalibration is necessary]. We can use capacitors too (using their exponential charging/discharging equations) or a linear optocoupler like MOC5010.
  • Software: writing some code snippets to Matlab/Python programs 
  • Using a Foster-Seeley phase discriminator: However, a new algorithm should be developed.
  • Converting the electrical signals to mechanical tracings on a rotating Kymograph [speed adjusted] may make it easier to read and count
  • Allowing only signals above a certain 'predefined' threshold voltage to pass through. We may use diodes for this cut-off estimation. Next, employ a CD 4520, a dual 4 BIT binary up counter that advances from LOW to High transition on clock input '0' (CK0) when CK1 is high, after the signal has been "gate"d . We can use an appropriate crystal to this counting purpose. Many optically based circuits are available on the net.
  • We can think of using a frequency to voltage converter IC like LM 2907
  • But presently, i'll be counting them manually. My time limitations and fading electronic experiences precludes any pursuits of above kind.
After we have successfully counted the 'rates' of 'action potential's, we can plot their number/spikes vs time plot in a linear or logarithmic scale. 


Here's where I positioned the ground electrode, on the manubrium sterni, on the upper chest (breastbone). The overlying hairs had been shaved and cleaned with spirit to reduce the input impedance. In all the spikerbox experiments the placement of the ground remained the same unless otherwise stated. 

To be continued....

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This work by Amiya Sarkar is licensed under a Creative Commons Attribution 4.0 International License.
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