BioBoard/Documentation/Optical loss

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Introduction to optical loss

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 (spectro)photometry, the analysis of the reflection or transmission properties of a material as a function of wavelength. Basically, this means that shining light of a known wavelength through a substance can be used to derive lots of information about the substance. To do this, you need a photometer - an instrument for measuring light - which is essentially a combination of a light source and a light sensor, where you can control the intensity and wavelength of the light, the distance the light has to traverse, and measure how much light was absorbed and/or scattered by the sample (optical loss).

In biology, optical loss is often used as a proxy measurement for biomass (especially in liquid cultures), which can otherwise be somewhat troublesome and time consuming to measure. Commonly used techniques include: counting cells in a special microscope chamber, marking cells with radioactive isotopes and using scintillation counting, incubating on solid substrates overnight and counting the resulting colonies, and 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. For instances, measuring the light absorption of chlorophyll in an algae vat may be used as a direct proxy for the algal density, and doing so repeatedly over time thus provides a data set which reflects the biological growth.

Building an NIR probe

Light source and light sensor pairing

Discussion of pros/cons of different source/sensor pairs

What you need

  • IR LED
  • Phototransistor
  • 1kΩ resistor
  • 100Ω resistor
  • Wire
  • Soldering iron + solder
  • ¾" acrylic tube
  • ¾" acrylic discs
  • Acrylic cement (thick)
  • 1" PVC pipe
  • Aquarium glue/hot glue

Optional: cell-phone motor (BubbleShaker Technology)

How to build it

Cutting acrylic and PVC

Drilling holes

Soldering wires

Fixing diodes

Glueing discs on tubes

Plugging tubes

Covering it up

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

Reduction of light passing through a mass

Absorbance vs. scattering


  • Optek
  • Wikipedia
  • TruCell .pdf
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