BioBoard/Documentation/Optical loss

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=Introduction to optical loss=
 
=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 [http://en.wikipedia.org/wiki/Spectrophotometry (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 [http://en.wikipedia.org/wiki/Photometer 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).
+
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 [http://en.wikipedia.org/wiki/Spectrophotometry 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 [http://en.wikipedia.org/wiki/Photometer 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.
  
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.
+
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 [http://en.wikipedia.org/wiki/Infrared#Different_regions_in_the_infrared 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 [http://www.optek.com/Schematic_Single_Channel_NIR_LED_Probe.asp single-channel NIR sensor] from Optek, which emits and detects at 850nm, and is designed for in-line monitoring of yeast fermentations.
  
  
=Building an NIR probe=
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=Building a NIR probe=
  
Light source and light sensor pairing
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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
 
Discussion of pros/cons of different source/sensor pairs
 +
 +
This design uses an 850nm plastic LED 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==
 
==What you need==
Line 70: Line 77:
  
 
=Geeking out=
 
=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 [http://en.wikipedia.org/wiki/Spectrophotometry 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
 
Reduction of light passing through a mass

Revision as of 22:55, 28 April 2011

Contents

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 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

  • 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...

Calibrating

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

Links

  • Optek
  • Wikipedia
  • TruCell .pdf
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