Difference between revisions of "Team:Aachen/Notebook/Construction Manuals/Biomass Sensor"

 
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__NOTOC__
 
__NOTOC__
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To build your own continous OD device several components and some working steps are needed. Of those this page will inform you.
+
To build your own continous OD device several components and some working steps are needed. This page will inform you of the same.
  
  
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==TSL 235 R==
 
==TSL 235 R==
 
{{Team:Aachen/Figure|size=small|Aachen_PhotoTransistor.JPG|title=TSL 235 R}}
 
{{Team:Aachen/Figure|size=small|Aachen_PhotoTransistor.JPG|title=TSL 235 R}}
−
The TSL 235 R is a light to frequency converter. The higher the intensity of the light, the higher is the frequency of an oscillating signal the transistor gives on the signal pin. Every time the signal rises from the minimum to the maximum we have a so-called rising edge. In the Arduino each of those rising edges causes an interrupt and an interrupt function that increments a counter is executed. After a determined time we check how high this counter has risen, send this value to the MCP and set the counter to zero to count the edges in the next measunring interval.  
+
The TSL 235 R is a light to frequency converter. The higher the intensity of the light, the higher is the frequency of an oscillating signal given out by the transistor on the signal pin. Every time the signal rises from the minimum to the maximum, we have a "rising edge". In the Arduino each of those rising edges causes an interrupt and thereby an interrupt function that increments a counter is executed. After a determined time we check how high this counter has risen, send this value to the MCP and set the counter to zero to count the edges in the next measuring interval.  
  
−
This procedure is known as frequency counting. With a higher OD the intensity of light falling onto the transistor decreases and we count lesser values. In the MCP the transmitted values are compared to a calibration curve and hereby we can determine the OD of the liquid.
+
This procedure is known as frequency counting. With a higher OD the intensity of light falling onto the transistor decreases and we count lesser values. In the MCP the transmitted values are compared to a calibration curve and hence we can determine the OD of the liquid.
  
−
To get more precise values we can increase the measurement time in the Arduino firmware, with lesser times we get values more frequent. But everytime we change the measurement time, we have to calibrate the device again.
+
To get more precise values we can increase the measurement time in the Arduino firmware, with lesser times we get values more frequent. But every time we change the measurement time, the device needs to be calibrated again.
  
 
==LED Dialight 5502505F==
 
==LED Dialight 5502505F==
 
{{Team:Aachen/Figure|size=small|Aachen_LED_Side_1.JPG|title=TSL 235 R}}
 
{{Team:Aachen/Figure|size=small|Aachen_LED_Side_1.JPG|title=TSL 235 R}}
−
The used LED emits light with a spectrum at around 600 nm. As in biology for OD measurement mostly 605 nm is used, we attach a red filter with a transmiitance peak at this wavelenght to measure with the same wavelenght as in common OD devices.  
+
The used LED emits light with a spectrum having a center frequency of 600 nm. OD measurement in biology uses 605 nm most frequently, we attach a red band pass filter with a transmittance peak at this wavelength to measure with the same wavelength as in the commonly found OD devices.  
−
If the LED is operated with too much current it will get destroyed. To avoid this it is necessary to use a 180 Ohm resistor in series with the LED when we connect it to the 5 V of the Arduino.
+
If the LED is operated with excess current it can get destroyed. To avoid this it is necessary to use a 180 Ohm resistor in series with the positive pin of the LED, which is connected to the 5 V of the Arduino.
 +
 
 +
 
 +
 
 +
 
  
 
=Assembly=
 
=Assembly=
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==LED==
 
==LED==
 
{{Team:Aachen/Figure|size=small|Aachen_LED_Pins_1.png|title=Pinout for the LED}}
 
{{Team:Aachen/Figure|size=small|Aachen_LED_Pins_1.png|title=Pinout for the LED}}
−
# Bend up the pins, comming out of the LED.  
+
# Bend up the pins, coming out of the LED.  
−
# Take a red and a blue wire, cut the connectors on one end of each wire and pull thinn shrink tubes (1 cm length) over the cut end. Then pull a bigger shrink tube (3 - 4 cm length) over both of the wires.
+
# Take a red and a blue wire, cut the connectors on one end of each wire and pull thin shrink tubes (1 cm length) over the cut end. Then pull a bigger shrink tube (3 - 4 cm length) over both of the wires.
−
# Solder the red wire to the positive pin (VDD)(see picture) and the blue one to the negative pin (GND). The easiest way to solder the wires and to avoid the LED from heating up is first to apply some soldering tin on the cut ends of the wires and only then connect it to the pins of the LED with short touches of the soldering iron. After each soldering place the thinn shrink tube over the soldered connection between LED and wire and heat the tube until it shrinks.  
+
# Solder the red wire to the positive pin (VDD)(see picture) and the blue one to the negative pin (GND). The easiest way to solder the wires and to avoid the LED from heating up is to first apply some soldering tin on the cut ends of the wires and only then connect it to the pins of the LED momentarily touching the soldering iron. After soldering each pin, pull the thin shrink tube over the soldered connection between LED and wire and heat the tube until it shrinks.  
−
# Pull the big shrink tube over the smaller ones and shrink it. The small shrink tubes are necessary to avoid short circuits and the big one stabilizes the connection.
+
# Pull the bigger shrink tube over the smaller ones and shrink it. The small shrink tubes are necessary to avoid short circuits and the big one stabilizes the connection.
−
# Before connecting the LED to any voltage source make sure that a proper resistor is in series with the LED. In case of the provided circuit the 180 Ohm resistor is suitable and must be placed in the designated position.
+
# Before connecting the LED to any voltage source make sure that a proper resistor is in series with the LED. In case of the provided circuit, the 180 Ohm resistor is suitable and must be placed in the designated position.
−
# in the provided circuit the wires must be plucked in the designated connectors. If you use another circuit, the red red wire goes to 5V and the blue wire to ground, but take care of a resistor in series.
+
# In the provided circuit the wires must be plugged to the designated connectors. If you use another circuit, the red red wire goes to 5V and the blue wire to ground, but you should take care of a resistor in series.
  
 
==Photo transistor==
 
==Photo transistor==
  
 
{{Team:Aachen/Figure|size=small|Aachen_PhotoTransistor_Pins_1.png|title=Pinout for the photo transistor}}
 
{{Team:Aachen/Figure|size=small|Aachen_PhotoTransistor_Pins_1.png|title=Pinout for the photo transistor}}
−
# Carefully bend the connectors by 90 degree that they stand at right angles to the head of the transistor.
+
# Carefully bend the connectors by 90 degree so that they stand at right angles to the head of the transistor.
−
# Take a red, a blue and a green wire and cut the connectors one one end of each wire and pull thinn shrink tubes (1 cm length) over the cut ends. Then pul a bigger shrink tube over all three wires.
+
# Take a red, a blue and a green wire and cut the connectors to one end of each wire and pull thin shrink tubes (1 cm length) over the cut ends. Then pull a bigger shrink tube over all three wires.
−
# Solder the red wire to the positive pin (VDD)(see picture), the blue one to the negative pin (GND) and the green one to the signal pin (SIGNAL). The easiest way to solder the wires and to avoid the LED from heating up is first to apply some soldering tin on the cut ends of the wires and only then connect it to the pins of the transistor with short touches of the soldering iron. After each soldering place the thinn shrink tube over the soldered connection between transistor pin and wire and heat the tube until it shrinks.  
+
# Solder the red wire to the positive pin (VDD)(see picture), the blue one to the negative pin (GND) and the green one to the signal pin (SIGNAL). The easiest way to solder the wires and to avoid the transistor from heating up is to first apply some soldering tin on the cut ends of the wires and only then connect it to the pins of the transistor with short touches of the soldering iron. After each soldering place the thin shrink tube over the soldered connection between transistor pin and wire and heat the tube until it shrinks.  
 
# Pull the big shrink tube over the smaller ones and shrink it. The small shrink tubes are necessary to avoid short circuits and the big one stabilizes the connection.
 
# Pull the big shrink tube over the smaller ones and shrink it. The small shrink tubes are necessary to avoid short circuits and the big one stabilizes the connection.
 
# Connect the wires to the designated connectors if you use the provided circuit. Else the red wire must be connected to 5V, the blue wire to ground and the green wire provides the oscillating signal.
 
# Connect the wires to the designated connectors if you use the provided circuit. Else the red wire must be connected to 5V, the blue wire to ground and the green wire provides the oscillating signal.
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==Glass structure==
 
==Glass structure==
  
−
# Cut the thinn end of the HPLC vial inlet with a drill and a cutting disk.
+
# Cut the thin end of the HPLC vial inlet with a drill and a cutting disk.
−
# Apply the thinn black silicon tube at the cut, thinn end of the vial inlet and the thick tube at the thick end. The thinn end has to have length around 3 cm.
+
# Apply the thin black silicon tube at the cut, thin end of the vial inlet and the thick tube at the thick end. The thin end has to have length around 3 cm.
 +
 
  
  
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To assemble the device need not to be attached to the circuit.
 
To assemble the device need not to be attached to the circuit.
−
# Drip a drop of hot glue in the holes for the transistor and the LED structure of one of the brackets and place the prepared structures. Take care that the light can fall optimal through the light channel.
+
# Drop hot glue in the holes for the transistor and the LED structure of one of the brackets and place the prepared structures. Take care that the light can fall optimally through the light channel.
−
# Press a needle into the septum and connect the thinn black silicon tube of the glass structure to the needle. Apply all the other tubes and autoclave the whole system.
+
# Press a needle into the septum and connect the thin black silicon tube of the glass structure to the needle. Apply all the other tubes and autoclave the whole system.
 
# Cut a 1.5 cm x 2 cm piece from the red filter, wrap it around the vial inlet and fix it with a transparent glue strip.
 
# Cut a 1.5 cm x 2 cm piece from the red filter, wrap it around the vial inlet and fix it with a transparent glue strip.
−
# Pull the tubes through the hole in the OD fastening structure and place the vial inlet in the designated hole. Then place the other bracket and fasten it with four M3 screws.
+
# Pull the tubes through the hole between the two OD brackets and place the vial inlet in the designated hole. Then place the other bracket and fasten it with four M3 screws.
 
# Attach the wires to the designated connectors.
 
# Attach the wires to the designated connectors.
  
−
=References=
+
{{Team:Aachen/Video|ogg=https://static.igem.org/mediawiki/2015/b/bc/Aachen_Bioreactorvideo_Od.ogg|mp4=/wiki/images/7/72/Aachen_OD.mp4|title=Continuous OD Device|subtitle=Steps to construct and run your very own continuous Optical Density Measuring Device|size=large}}
  
 +
=Files=
 +
The 3D structure can be found here : [https://static.igem.org/mediawiki/2015/9/91/Aachen_OD_Module.zip Aachen_OD_Module.zip]
 +
 +
The Arduino Firmware can be found here : [https://static.igem.org/mediawiki/2015/8/8c/Aachen_OD_final.zip Aachen_OD_final.zip]
 +
 +
The Assembly Video can be found here : [https://static.igem.org/mediawiki/2015/8/8c/Aachen_OD_final.zip Aachen_OD_final.zip]
 +
 +
=References=
  
 +
<references/>
  
  
 
{{Team:Aachen/Footer|color=yellow}}
 
{{Team:Aachen/Footer|color=yellow}}

Latest revision as of 03:30, 19 September 2015


To build your own continous OD device several components and some working steps are needed. This page will inform you of the same.


Materials required

  • Electrical:
    • 1 LED Dialight 5502505F[1]
    • 1 TSL 235 R photo transistor[2]
    • 1 180 Ohm resistor
    • several wires with male endings in at least three different colours (red, blue and green are prefered)
    • shrink tubes with different diameters
    • a soldering iron and soldering tin
  • Mechanical and biological:
    • 2 3D printed brackets
    • 4 M3 screws (20 mm long)
    • black silicon tube (inner diameter 1 mm)
    • black silicon tube (inner diameter 3 mm)
    • 1 HPLC vial inlet
    • transparent and flexible filter with a transmittance peak at around 605 nm
    • transparent glue strips
    • hot glue or plastic glue

TSL 235 R

Aachen PhotoTransistor.JPG
TSL 235 R

The TSL 235 R is a light to frequency converter. The higher the intensity of the light, the higher is the frequency of an oscillating signal given out by the transistor on the signal pin. Every time the signal rises from the minimum to the maximum, we have a "rising edge". In the Arduino each of those rising edges causes an interrupt and thereby an interrupt function that increments a counter is executed. After a determined time we check how high this counter has risen, send this value to the MCP and set the counter to zero to count the edges in the next measuring interval.

This procedure is known as frequency counting. With a higher OD the intensity of light falling onto the transistor decreases and we count lesser values. In the MCP the transmitted values are compared to a calibration curve and hence we can determine the OD of the liquid.

To get more precise values we can increase the measurement time in the Arduino firmware, with lesser times we get values more frequent. But every time we change the measurement time, the device needs to be calibrated again.

LED Dialight 5502505F

Aachen LED Side 1.JPG
TSL 235 R

The used LED emits light with a spectrum having a center frequency of 600 nm. OD measurement in biology uses 605 nm most frequently, we attach a red band pass filter with a transmittance peak at this wavelength to measure with the same wavelength as in the commonly found OD devices. If the LED is operated with excess current it can get destroyed. To avoid this it is necessary to use a 180 Ohm resistor in series with the positive pin of the LED, which is connected to the 5 V of the Arduino.



Assembly

LED

Aachen LED Pins 1.png
Pinout for the LED
  1. Bend up the pins, coming out of the LED.
  2. Take a red and a blue wire, cut the connectors on one end of each wire and pull thin shrink tubes (1 cm length) over the cut end. Then pull a bigger shrink tube (3 - 4 cm length) over both of the wires.
  3. Solder the red wire to the positive pin (VDD)(see picture) and the blue one to the negative pin (GND). The easiest way to solder the wires and to avoid the LED from heating up is to first apply some soldering tin on the cut ends of the wires and only then connect it to the pins of the LED momentarily touching the soldering iron. After soldering each pin, pull the thin shrink tube over the soldered connection between LED and wire and heat the tube until it shrinks.
  4. Pull the bigger shrink tube over the smaller ones and shrink it. The small shrink tubes are necessary to avoid short circuits and the big one stabilizes the connection.
  5. Before connecting the LED to any voltage source make sure that a proper resistor is in series with the LED. In case of the provided circuit, the 180 Ohm resistor is suitable and must be placed in the designated position.
  6. In the provided circuit the wires must be plugged to the designated connectors. If you use another circuit, the red red wire goes to 5V and the blue wire to ground, but you should take care of a resistor in series.

Photo transistor

Aachen PhotoTransistor Pins 1.png
Pinout for the photo transistor
  1. Carefully bend the connectors by 90 degree so that they stand at right angles to the head of the transistor.
  2. Take a red, a blue and a green wire and cut the connectors to one end of each wire and pull thin shrink tubes (1 cm length) over the cut ends. Then pull a bigger shrink tube over all three wires.
  3. Solder the red wire to the positive pin (VDD)(see picture), the blue one to the negative pin (GND) and the green one to the signal pin (SIGNAL). The easiest way to solder the wires and to avoid the transistor from heating up is to first apply some soldering tin on the cut ends of the wires and only then connect it to the pins of the transistor with short touches of the soldering iron. After each soldering place the thin shrink tube over the soldered connection between transistor pin and wire and heat the tube until it shrinks.
  4. Pull the big shrink tube over the smaller ones and shrink it. The small shrink tubes are necessary to avoid short circuits and the big one stabilizes the connection.
  5. Connect the wires to the designated connectors if you use the provided circuit. Else the red wire must be connected to 5V, the blue wire to ground and the green wire provides the oscillating signal.

Glass structure

  1. Cut the thin end of the HPLC vial inlet with a drill and a cutting disk.
  2. Apply the thin black silicon tube at the cut, thin end of the vial inlet and the thick tube at the thick end. The thin end has to have length around 3 cm.



Assembling the device

To assemble the device need not to be attached to the circuit.

  1. Drop hot glue in the holes for the transistor and the LED structure of one of the brackets and place the prepared structures. Take care that the light can fall optimally through the light channel.
  2. Press a needle into the septum and connect the thin black silicon tube of the glass structure to the needle. Apply all the other tubes and autoclave the whole system.
  3. Cut a 1.5 cm x 2 cm piece from the red filter, wrap it around the vial inlet and fix it with a transparent glue strip.
  4. Pull the tubes through the hole between the two OD brackets and place the vial inlet in the designated hole. Then place the other bracket and fasten it with four M3 screws.
  5. Attach the wires to the designated connectors.


Continuous OD Device
Steps to construct and run your very own continuous Optical Density Measuring Device

Files

The 3D structure can be found here : Aachen_OD_Module.zip

The Arduino Firmware can be found here : Aachen_OD_final.zip

The Assembly Video can be found here : Aachen_OD_final.zip

References

  1. ↑ http://www.dialight.com/Assets/Brochures_And_Catalogs/Indication/550-xx05-004.pdf
  2. ↑ http://www.ti.com/lit/ds/symlink/tsl235.pdf


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