BioBoard/Documentation/Optical loss

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Introduction to optical loss

When light travels through a substance, whether it's solid, liquid or gaseous, the intensity of the light is reduced; this is called optical loss. Measuring how much the light intensity is reduced at different wavelengths is called spectrophotometry, and can be used to determine many different properties of the substance, such as concentration of a solution or opacity of a glass pane. To do this, you need a photometer, which is essentially a combination of a light source of known intensity and wavelength, and a light sensor which measures how much light was absorbed and/or scattered by the sample over a fixed gap.

Spectrophotometry may also be applied to gain information about biological processes. Especially in microbiology, where most work is done with organisms that are too small and too numerous to easily count individually, optical loss is often used as a proxy for cell density or biomass. For instance, measuring the light absorption of chlorophyll in an algae vat may be used as a direct proxy for the algal density.

In industrial production systems, such as large-scale alcohol fermentation, insulin production, etc., biological growth is often monitored using in-line ('live') sensors, which measure optical loss, usually at wavelengths in the near-infrared (NIR) or IR-A spectrum (700-1400nm). The inspiration for the home-built NIR probe described in the rest of this wiki is a single-channel NIR sensor from Optek, which emits and detects at 850nm, and is designed for in-line monitoring of yeast fermentations.

Building a NIR probe

When building a near-infrared sensor, the first important choice is that of light source (photoemitter) and sensor (photosensor). Important considerations include:

  • what's the appropriate wavelength(s) for your purposes?
  • how much circuitry do you want to build?
  • how much can you afford to invest?

Discussion of pros/cons of different source/sensor pairs

This design uses an 850nm plastic LED (Everlight HIR204) as the photoemitter, and a matching phototransistor (Optek OP506B) as the photosensor. The transistors cost 80 cents each, and the required circuitry is limited to a couple of resistors.

What you need

  • 1x IR LED
  • 1x Phototransistor
  • 1x 1kΩ resistor
  • 1x 100Ω resistor
  • 1x Soldering iron + solder
  • 1x 3/4" / 20mm acrylic tube
  • 4x 3/4" / 20mm acrylic discs
  • 1x 1" / 25mm PVC pipe
  • Acrylic cement (thick)
  • Wire
  • Aquarium glue/hot glue

Optional: cell-phone motor (BubbleShaker Technology)

How to build it

Step 1: Cutting acrylic

Start by cutting the 3/4" acrylic tube into 2 x 1" / 25mm pieces (A1 and A2) and 1 x 3/4" / 20mm piece (A3). Make a slit in A3 approx. 1/3" / 8mm wide by making two cuts that run the entire length of the tube.

Step 2: Soldering wires

Cut the leads on both the LED and the phototransistor about 30% shorter. Solder wires onto the leads, and make sure to note down what colour wire you use for the different leads! These are polar devices and won't work if you wire them up backwards. We suggest you use red for both positive / power / emitter leads, black for the negative / ground lead on the LED, and white for the collector lead on the phototransistor.

Step 3: Drilling holes and fixing diodes

Drill a 3mm (or as close as you can get with Imperial units) hole in the center of each acrylic disc. Take two of the discs, carefully lay down a narrow line of acrylic cement around the holes, then insert the LED and phototransistor in the holes, and set them aside to cure.

Step 4: Assembling and sealing

When the acrylic discs with the LED and phototransistor have properly cured, thread A1 and A2 on one set of wires each, lay a fat line of acrylic cement along the edge of both discs and press A1 and A2 firmly into place, creating a lidded, cylindrical chamber for the leads. Leave to cure. Reinforce the seal by laying down another line of acrylic cement along the joint between the tubes and the discs.

Step 5: Covering it up with PVC

Step 1: NIR probe parts

Things to keep in mind

Biologically inert materials

Food safety

Aquarium glue vs hot glue

Interfacing and measuring

Arduino sketch should go here...


How to find out whether your measurements are accurate (do you need to know?)

How to adjust (distance, resistance)

Making it cooler

Tuning to different substances

Multi-channel measurements

Geeking out

In chemistry and biology, many different methods are employed to analyze the properties of a given substance. One method that is extremely useful in both disciplines is spectrophotometry, the analysis of reflection or transmission properties of a material as a function of wavelength.

techniques can be split into in-line ('live')

  • counting cells in a special microscope chamber,
  • marking cells with radioactive isotopes and counting scintillation events

and off-line

  • incubating on solid substrates overnight and counting the resulting colonies
  • desiccating samples to measure total dry organic matter

None of these techniques are very useful for monitoring biological growth over time, however, so photometry is often used instead.

Reduction of light passing through a mass

Absorbance vs. scattering


  • Optek
  • Wikipedia
  • TruCell .pdf
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