BioBoard/Documentation/Optical loss: Difference between revisions
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=Introduction to optical loss= | =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 [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. | |||
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 | =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 | 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
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