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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. | 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 a NIR probe= | =Building a NIR probe= | ||
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*how much can you afford to invest? | *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 - $0.43) as the photoemitter, and a matching phototransistor (Optek OP506B - $0.80) as the photosensor; the required circuitry is limited to a couple of resistors. | |||
==What you need== | ==What you need== | ||
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Optional: cell-phone motor (BubbleShaker Technology) | Optional: cell-phone motor (BubbleShaker Technology) | ||
==How to build it== | ==How to build it== | ||
[[File:IMG259.jpg|200px|thumb|right|Step 1: probe parts]] [[File:NIRprobe2.jpg|200px|thumb|Step 3: assembling]] [[File:NIRprobe3.jpg|200px|thumb|right|Step 4: waterproofing]] [[File:NIRprobe4.jpg|200px|thumb|right|Step 5: spacing]] | [[File:IMG259.jpg|200px|thumb|right|Step 1: probe parts]] [[File:NIRprobe2.jpg|200px|thumb|Step 3: assembling]] [[File:NIRprobe3.jpg|200px|thumb|right|Step 4: waterproofing]] [[File:NIRprobe4.jpg|200px|thumb|right|Step 5: spacing]] | ||
'''Step 1: Cutting acrylic''' | '''Step 1: Cutting acrylic''' | ||
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'''Step 5: Spacing''' | '''Step 5: Spacing''' | ||
Once the aquarium / hot glue has cured properly, take A3, place it between the two acrylic discs holding the LED and | Once the aquarium / hot glue has cured properly, take A3, place it between the two acrylic discs holding the LED and photoresistor, and glue the three parts together with acrylic cement, then leave to dry. | ||
'''Step 6: Blocking sunlight with PVC (optional)''' | '''Step 6: Blocking sunlight with PVC (optional)''' | ||
Since sunlight includes lots of infrared radiation, it may be necessary to shield your probe. A very simple way of doing this is to take | Since sunlight includes lots of infrared radiation, it may be necessary to shield your probe. A very simple way of doing this is to take a dark plastic cup that's deep enough to fit the whole assembly, drill a small hole in the bottom of the cup, then turn it upside down, pull the wires through the hole, and use the cup for an inverse lampshade. | ||
''' | '''Step 7: Building the BubbleShakerTM (optional)''' | ||
==Things to keep in mind== | |||
Biologically inert materials | |||
Food safety | |||
Aquarium glue vs hot glue | |||
=Interfacing and measuring= | =Interfacing and measuring= | ||
[[ | After assembling the probe, you'll need to wire it up to some kind of microcontroller; we've used an Arduino clone called [http://www.ladyada.net/make/boarduino/ BoArduino], and will use that as example, but you can use any type you like. In order to program the the BoArduino, you have to download and install the [http://arduino.cc/en/Main/Software Arduino software] first. Once this is done, you're ready to connect your board - in some cases, this requires a special cable, so make sure you've got the right one! Now open the Arduino program, copy the code in the box below into the blank sketch, and hit upload. Open the serial monitor to see the print-out of the data being transmitted from the probe, which ought to look more or less like this: @NIR:0:0.99$. | ||
// | |||
// This Arduino sketch reads our custom NIR absorption sensor. | |||
// | |||
// This code is part of the BioBridge Project. | |||
// | |||
// | |||
// author: rolf van widenfelt (c) 2011 | |||
// | |||
// revision history: | |||
// | |||
// apr 25, 2011 - rolf | |||
// identify this probe. (needed for BioBoard protocol) | |||
// | |||
// apr 17, 2011 - rolf | |||
// created. | |||
// ADC code seems to work.. still need to connect actual sensor and document connections! | |||
// | |||
// | |||
// code modification: | |||
// you will need to set some calibration points... (FILL THIS IN!!) | |||
// | |||
// description: | |||
// this sketch will periodically output a short string that contains the NIR transmittance | |||
// along with some other fields that indicate which probe (0) is being read. | |||
// the string should look like this for a transmittance of 99% : | |||
// | |||
// @NIR:0:0.99$ | |||
// | |||
// this is output periodically. (in this case, every 5 sec) | |||
// | |||
// In the case of an error, an "E" message is output instead of the temperature, like this: | |||
// | |||
// @TC:0:EBADVALUE$ | |||
// | |||
// note that these data packets are output to the serial console window at 19200 baud. | |||
// also, when the sketch first starts, it identifies the software and version, like this: | |||
// | |||
// @ID:BIOBOARD:TESTBATCH1:1.1$ | |||
// | |||
// that's it! | |||
// | |||
static const char ProjectName[] = "TESTBATCH1"; | |||
const int analogNIRPin = A0; // analog input pin that the NIR phototransistor circuit is connected to | |||
// CALIBRATION SETTINGS | |||
#define IMAX 4.9 /* max phototransistor current with IR LED on (no obstructions, just 1inch air) */ | |||
#define IMIN 0.02 /* dark current (NOTUSED) */ | |||
#define VMAX 5.0 /* arduino voltage = 5.0v */ | |||
#define ADCMAX 1023 /* highest ADC value */ | |||
#define IMAXI (ADCMAX*IMAX/VMAX) /* highest ADC value we expect from our sensor */ | |||
#define IMAXI_INV (1.0/(ADCMAX*IMAX/VMAX)) /* inverse (this avoids a divide during runtime) */ | |||
void setup(void) | |||
{ | |||
// start serial port | |||
//Serial.begin(9600); | |||
Serial.begin(19200); | |||
Serial.print("\n\r@ID:BIOBOARD:"); | |||
Serial.print(ProjectName); | |||
Serial.print(":0.1$\n\r"); | |||
// configure ADC to use external 5v reference (default) | |||
analogReference(DEFAULT); | |||
// just in case, throw away 1st ADC read | |||
(void) analogRead(analogNIRPin); | |||
// identify this probe | |||
Serial.print("@PR:NIR:0$\n\r"); | |||
} | |||
void printNIR() | |||
{ | |||
int sensor = analogRead(analogNIRPin); | |||
float sample = IMAXI_INV * sensor; | |||
if (sensor > IMAXI + 10) { | |||
Serial.print("EBADVALUE"); // oops, value is clearly wrong, so output an "E" message. | |||
} else { | |||
Serial.print(sample); | |||
} | |||
// XXX debug - we output raw ADC value as well | |||
Serial.print(":"); | |||
Serial.print(sensor); | |||
} | |||
void loop(void) | |||
{ | |||
delay(2500); | |||
Serial.print("@NIR:0:"); | |||
printNIR(); | |||
Serial.print("$\n\r"); | |||
} | |||
=Calibrating= | =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 [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 | |||
Absorbance vs. scattering | |||
=Links= | =Links= | ||
*Optek | |||
* | *Wikipedia | ||
*TruCell .pdf | |||
* | |||
* |