Experimental setup

Before starting to record electrical signals you’ll need a suitable sample. For example, slime (Physarum) tube growing across two electrodes inside enclosure, see below:

The instrumentation can be connected to aluminium foil electrodes via flying leads and crocodile clips, see example below:

The polarity of the connections is not normally important but try keep the flying leads close together (or twisted) to reduce background electrical noise.

For light sensitive samples cover them to reduce the affect of changing light levels during recordings.

The USB cable need to be plugged into USB port on your computer/device.

 

Recording method can be: 

(a) manual for guidance click here

(b) automatically’ via PhyLink Processing software for guidance click here

 

Example recording of Physarum tube

Sample W1 was connected to PhyLink unit via flying leads and kept semi-dark (with cardboard cover) on open bench (no Faraday Cage).

PhyLink hardware (analogue to digital converter) was running Arduino sketch V18.

Example recording in comma-separated values (CSV) format (recorded at 16 samples per second) can be downloaded by clicking link below:

Example_trace_W1

 

Example of manual analysis

(a) Recording of voltage against time viewed with SigView (or equivalent software) see below:

(b) Select the measurements over the period of time of interest and analyse via FFT

Average fundamental frequency for selected period of time was c. 8.2 mHz.

(c) The fundamental frequency of oscillation will change over time (depending on several factors including environmental conditions and stimuli). The change in frequency over time can be determined by FFT analysis of different periods, see example below:

In this particular example, the fundamental frequency of oscillation after the tube formed was ~7.1 mHz which increased to ~8.2 mHz and then reduced to ~7mHz.

Applying a stimuli (such as food) would affect the fundamental frequency. Therefore the properties of the food (or other stimuli) can be inferred by monitoring the slime’s fundamental frequency of oscillation over prolonged time. In other words, the fundamental frequency should be measured before, during and after the stimuli is applied to know the relative change.

 

Analysis with PhyLink code

Open PhyLink Processing code (V17) on your computer/device.

Click “Read recorded measurements from saved file or shared database” icon and then click ‘tick’ icon as shown below:

Click the ‘Path and File name to save FFT values’ icon as shown below:

Select the folder and enter the file name to save FFT values as shown in example below:

Click ‘Select the path and file where your database exists’ icon as shown below:

Select folder and click on file of previously recorded/saved measurement values, as shown in example below:

Click on ‘Save’ and you’ll be asked to ‘Confirm Save As’ as shown below:

You’ll then be asked to enter three settings for analysis:

For ‘number of BINS enter: 1024

For ‘duration’ enter: 30 (this will vary with duration of saved recording)

For ‘samples per second’ enter: 16

Then click the ‘start’ icon, as shown in example below:

PhyLink Processing code will begin analysis of the recorded/saved voltage measurements, see example below:

It may take some time to calculate fundamental frequency of oscillation for erratic recordings.

Depending on the consistency and level of background noise the fundamental frequency of oscillation cannot always be determined.

Rule of thumb: 8 or more consistent cycles required for FFT to calculated fundamental frequency of oscillation

Click the ‘camera’ icon at any time to save screenshot(s) as shown below: