Micro-electro-physiology @ HAIP, Ljubljana

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Revision as of 12:55, 29 November 2010 by Dusjagr (talk | contribs) (On Measuring)
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Background Info

Electrochemistry of Plant Life

Electrochemistry Encyclopedia

Video of extracellular measurement of action potential of the venus flytrap

Protocols

On Measuring

Analog to Digital Converter (ADC)

Arduino

Using the arduino we can measure analog voltages using the 6 Inputs ADC. The analog voltage between 0 and 5 V is converted into a 10bit digital number, from 0 to 1023. this can be used to read a value from a sensor, eg a temperature sensor such as the [slime_mold_culture.jpg TMP36], a potentiometer or from the electrodes.

Sound Card - Line In

If the potentials we want to measure are mostly changes/modulations in voltages, we can also use the analog-to-digital converter from the sound card. Although that means we cannot measure static voltages, but only fast changes changes, frequencies above ~ 1hz. The sound card is a very fast and precise ADC (single if mono, or double for stereo), sampling at 44khz or up to 96khz and 24 bit resolution.

Amplification

If the signals are to low, such as µV in the example of potentials in plants, we need to amplify the signal and make sure we do not have too much noise or other garbage in our signals. INA118 is a high end instrumental amplifier, with low noise. But maybe cheaper amp might do the trick aswell, such as the LM386

Multiplexing

If we want to measure more inputs we can multiplex them. meaning we measure one input at the time using a chip (4051), which got 8 inputs which are then routed to one single input on the arduino. read more about using the 4051 multiplexer/demultiplexer


Shielding

because every conducting wire, electrode or other parts of a measurement setup are also acting kinda as "antennas", its easy to pick up some artefacts, noise, humms from the electromagnetic environment. typical stuff the measure are the 50Hz humming from all the electric power and lamps or "biipbuupbiiiiip" from mobile phones. to prevent these one can use shielded cables or build a faraday cage around the whole setup.

DIY Glass Pipette Electrodes

Micro Electrode Arrays (MEA)

DIY Microscopy

To be able to observe the pipette we can build our own hacked digital microscopes, using cheap webcams, surveillance video cams or the PS3 eye. see more on the hackteria page.


Slime Mold

preparation of growth media


culture method

Slime mold culture.jpg

Slime 40h-5.jpg


Further links to Slimes

paper about growing slime mold as a map of japan

Plant S.M.E.L.A

Measuring things schematics.jpg

Setup

Plant smela v01.jpg

Experiments

Venus Fly Trap

Venus fly trap measurement.jpg


Slime Mold

Slime measurement.jpg


Recordings

testing the microsphone input from webcam as ADC

Measurements batterie2microphone cam.png

Media:test.mp3


slime-recording, but measuring something else

Measurements mobilephone.png

Media:Slime_smela-2.mp3

Patches for measuring

File:Galvanic synth.zip

Smela Patches

Participants

Marc Dusseiller, dusjagr labs

Špela Petrič,

Andrej Meglič,


rough schedule

Wednesday

  • Introduction
  • Experiments in manufacturing DIY electrodes
  • intro into DIY microscopy
  • using audio and pd for data measurement
  • using arduino and pd the measure/visualize data
  • start fungi cultures and preparations of plants
  • Setup of measurement setup


Thursday

  • Preparation of amplifiers and multiplexers
  • Setup of measurement setup
  • Experiments with plant recordings


Friday

  • Wrap-up Workshop: Introduction into all techniques developed
  • Preparations of individual pages for a publication using the diffusion layout.

Material for the Book

Example of book about DIY microscopy for Kids (german only)

Interesting Links

http://books.google.com/books?id=6a1_Gw8Tt10C&lpg=PR2&ots=AQKOZEm7Fn&dq=plant%20electrophysiology&pg=PR7#v=onepage&q&f=false

http://ediacaran.mech.northwestern.edu/neuromech/index.php/Main_Page

http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD1-4NC5T7P-2&_user=10&_coverDate=04%2F30%2F2007&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=ea73d908f93817a392f5f12ddebc6f72&searchtype=a


Preparations

Material to bring

Tools we need

Last minute orders