Basics of Instrumentation, Measurement and Analysis

Fall semester 2015, 4CP

Instructors: Tobi Delbruck (
                  Arko Ghosh (
                  Richard Hahnloser (
                  Giacomo Indiveri (
                  Shih-Chii Liu (
                  Valerio Mante (
                  Pawel Pyk (
                  Wolfger von der Behrens (
Coordination: Pawel Pyk

Time of the course: Tuesday 08:00 - 12:00

Location: Irchel room Y35 E30

Recommended literature
Franklin Bretschneider  &  Jan R. de Weille
Introduction to Electrophysiological Methods and Instrumentation 
Elsevier, 2006

Paul Horowitz & Winfield Hill
The Art of Electronics
Cambridge University Press, 1989



(to be populated)
Pawel Pyk

Introduction to electricity: electric charge, current and potential. Resistance, capacitance and inductance. Direct and alternating current. Frequency. Unwanted properties, impedance. Ohm and Kirchoff’s laws. Voltage and current measurements. Voltage divider. Resistors in practice THT i SMD. Resistor codes. E series.
Soldering introduction. Soldering and desoldering. Through-hole technology and surface mount technology. Lead free vs. leaded solder. Importance of soldering flux and cleaning. Solder wire and solder paste. Soldering Exercise 2015 and Exercise A 2015. 
Nice short tutorial Soldering Tutorial for Beginners: Five Easy Steps 
Manual: VOLTCRAFT_VC820-1_Digital-Multimeter.pdf



Pawel Pyk

Resistive analog sensors. Signal conditioning  before digitization (part 1 - the simple case of signal range matching). Digital to analog conversion (part 1 - multimeter).  Composition of unequal components: Filters. Response of high/low-pass RC-filters to the voltage step and sinusoidal wave. Capacitors in practice. Codes. Dielectrics capacitor dielectric comparison. Signal conditioning  before digitization (part 2 - filtering). Nyquist–Shannon sampling theorem. Digital to analog conversion (part 2 - oscilloscope). Exercise A 2015: sensors & Exercise B 2015: exploring characteristics of a simple passive low-pass and high-pass filters. Signals will be generated by the signal generator and analyzed with the help of oscilloscope.
Manuals: HP_33120A_Function_Generator.pdf, Tektronix_TDS420A_and_TDS460A_oscilloscopes.pdf.
Datasheets: Thermistor_RH16-6D502FB_Mitsubishi_Materials_Corporation.pdf, Flex_Sensor_Spectra_Symbol.pdf

Note B & W book is simplifying impedance formulas omitting the complex numbers - for proper equations see H & H p. 28 and  H & H pp. 31-32.

pp. 25-33 B & W
Exercise B 2015.pdf 

Pawel Pyk

Bipolar transistor. Emitter follower pp. 62-65 H & H. Common-emitter amplifier pp. 76-77 H & H. Classic transistor differential amplifier pp. 98-100 H & H. JFET and MOSFET transistors. Operational amplifier. Signal conditioning  before digitization (part 3 - amplifying). Digital to analog conversion (part 3 - PC).  Exercise C 2015: Building operational amplifier  band-pass filter for the microphone – microphone preamplifier. Test of the filter frequency response. Signal from the electret microphone consists from a constant shift from the ground about 0.9V and the alternative component in range of +/-50mV. To digitize such signal one should remove the constant component and very low frequencies (<20 Hz) from the signal by the high-pass filter. However, frequencies of most human speech harmonics lie above 100Hz, thus, we shall take the signal above this border. Afterwards one has to amplify it to make the output compatible with the standard audio recording equipment that has input range +/-1 V. Also, frequencies of most of harmonics in human speech lie below 10 kHz. Thus, we shall take the signal in frequency range 100 Hz - 10 kHz. We shall learn how to realize all these functions utilizing only one operational amplifier.
Datasheets: Amplifier_opa2350.pdf, Microphone_KPCM_G60H50_44DB_1184.pdf.
Some terms used in literature:
Q factorNodal analysis, Thévenin's theorem, re intrinsic emitter resistance

Pawel Pyk
Schematics and PCB design in Eagle. We will design electronics which will be later. Exercise D 2015 design schematics and PCB in Eagle. Designed PCB will be fabricated and used to build electronics in Exercise G 2015.
Richard Hahnloser
Digital filtering in Matlab. Ideal low-pass filter (fft), phase response, bidirectional filtering. Bessel, elliptic filter.
Pawel Pyk
Measuring high-resistance and low-capacitance. Exercise G 2015:   Building an impedance meter for microelectrodes, testing the impedance of metallic electrodes. Knowing the impedance of electrophysiological recording electrode is important for estimation of its recording capabilities – number of cells that can be recorded or separated, sensitivity to noise and etc. However, current that one should pass through such electrode for the measurement should not be too high: cells in the vicinity of the electrode tip can be destroyed. For the extracellular recording electrode the current should not exceed 30 nA. Most of electrical activity of single cells (spikes) lie in the frequency range 300-3000 Hz. Thus, to estimate suitability of the electrode to record such activity, its impedance is usually measured at 1 kHz. To measure the impedance of the microelectrode we shall generate 30nA sinusoidal current with the help of signal generator and current-limiting resistor. We shall estimate the impedance of the electrode by the voltage drop on it looking at the oscilloscope. Phase shift between the generator output and signal at the electrode will allow estimate resistive (active) and capacitive parts of electrode impedance separately. Preliminary measurement of voltage drop of at non-immerged in the solution (“virtual brain”) will allow to subtract the parasitic impedance of conductive wires to get precise estimate of the electrode impedance.
Pawel Pyk
Electrochemistry, electrolytes, AgCl electrode. Metal electrodes gold plating. Measuring electrode impedance before and after gold plating. Electrical processes in living organisms take place in watery solutions containing salts, proteins, carbohydrates and a host of other organic and non-organic substances. These processes are dominated to a large extent by various salts. Therefore, we will need a good understanding of the properties of electrolyte solutions and of the processes associated with them. In addition, most methods to get measurements from the wet medium are carried out with electronic instruments, which must be connected somehow to the process studied. Therefore, we are interested also in the processes at the electrodes used for measurement and stimulation. Exercise H 2015: Gold plating of the metal electrode. Measuring its impedance before and after gold plating. Fabrication of AgCl electrode by electrochemical oxidizing the silver wire in 0.5M KCl solution (forming silver chloride layer). Measuring I/V behavior of the electrode before and after oxidizing.
SIFCO Process Gold (Alkaline) Material Safety Data Sheet: MSDS-3023.pdf.
10.11 Shih-Chii Liu Preparing for data acquisition with Arduino.  
17.11 Giacomo Indiveri Measuring response properties from silicon neurons. Interfacing full-custom neuromorphic chips to computers for measuring current and voltage outputs from analog circuits that emulate neurons and synapses. Learning to use Keithley programmable voltage sources to provide bias values to the neuromorphic chip. Understanding the functionality of a low-power intergrate-and-fire neuron circuit. Measuring spikes and Frequency-Current transfer functions from the silicon neuron.


Tobi Delbruck

Basics of Arduino. Buying/using Arduino microcontroller boards/software development environment for acquiring analog signals e.g. from EMG, and producing digital output, e.g. for servo motor control.
01.12 Arko Ghosh Biosignals during interactions.  
08.12 Wolfger von der Behrens Processing of extracellular recordings. Raw data processing, filtering, spike detection, spike sorting, PSTH.
In this and next lecture you will implement all the steps that go from raw electrophysiology data to tuning curves of individual units.
15.12 Valerio Mante Dimensionality reduction, PCA, clustering, K-Means.  


Archive: Programs for Fall semester 2011, 2012, 2013, 2014

Please direct all questions to Pawel Pyk
Last updated September 13, 2015