# Team:Aachen/Notebook/Engineering/ODF

(Difference between revisions)
 Revision as of 20:34, 13 October 2014 (view source)Mjoppich (Talk | contribs) (→Development)← Older edit Latest revision as of 03:45, 18 October 2014 (view source)Nbailly (Talk | contribs) (→Saccharomyces cerevisiae) (185 intermediate revisions not shown) Line 1: Line 1: __NOTOC__ __NOTOC__ {{Team:Aachen/Header}} {{Team:Aachen/Header}} - + {{Team:Aachen/Stylesheet}} = OD/F Device = = OD/F Device = - == Development == + On this page we present the technical details of our OD/F Device. You can skip to specific chapters by clicking on the panels below: +
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+ - Building the OD/F device has been an interesting task. On the one hand, this device has been developed mainly by the IT division of our team. On the other hand, we got assistance from biologists suffering from color-blindness, yet eager to help selecting the best color filters for the LEDs. For the next year, you really have to select carefully who's going to help with which task! +
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+ General Considerations +

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• - === Measuring Principle === +
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+ OD Device +

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• - The measuring principle for both fluorescence and optical density (OD) measurement is depicted below. +
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+ F Device +

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• - {{Team:Aachen/FigureFlex|Aachen_odf_schemes.png|title=Setup of the measuring unit|subtitle=On the left, the setup of a classical spectrophotometer is depicted. The setup around the cuvette holder of our device is shown on the right.|width=400px}} + +
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+ DIY +

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+ + + {{Team:Aachen/BlockSeparator}} + + [[File:Aachen_14-10-10_ODF_Button_ipo.png|right|150px]] + + = General Considerations = + + + Building the OD/F Device has been an interesting task. While this device has been developed mainly by the IT division of our team, we got an immense support from the biologists suffering from color-blindness, yet eager to help selecting the best color filters for the LEDs. + The measuring principle and guidelines for this project have already been presented in the [http://2014.igem.org/Team:Aachen/OD/F_device project] section. + Here, details about selecting filters, code and a construction manual are presented. === Cuvette Holder === === Cuvette Holder === - The essential part of this device is the '''cuvette holder which has also been the most tricky thing to design'''. In short, we had to overcome a dilemma created by the need for an optimal height for the sensor: + The essential part of this device is the '''cuvette holder'''. In short, we had to overcome a dilemma created by the need for an optimal height for the sensor: * A too low sensor position bears problems with sedimentation as well as light diffraction from the bottom of the cuvette. * A too low sensor position bears problems with sedimentation as well as light diffraction from the bottom of the cuvette. * The sensor has to be as close as possible to the bottom so that enough light shines through for the fluorescence measurement. * The sensor has to be as close as possible to the bottom so that enough light shines through for the fluorescence measurement. - As a compromise, we place the sensor at a height of 0.75 cm, which, as it turned out later, is very close to one of the standard heights (0.2 cm, 0.8 cm, 1.2 cm) of OD meters. It is important to note that despite the official minimal fill height of 1.2 mL of the 1.5 mL cuvettes we used, our device also works with filling volumens of just 1 mL which in fact comes closer to reality in the lab. + As a compromise, we place the sensor at a height of 0.75 cm. It is comparable to one of the standard heights (0.2 cm, 0.8 cm, 1.2 cm) of OD meters. It is important to note that our device works with filling volumens of just 1 mL, which in fact comes close to reality in the lab. - The final cuvette holder design was rendered in a stl-file shown below: + The final cuvette holder design is rendered from a [http://2014.igem.org/Team:Aachen/Notebook/Engineering/Cuvette3D?action=raw stl-file] shown below: Line 30: Line 77: " width=500px height=500px frameBorder="0"> +
+ Cuvette Holder developed for our OD/F Device. - === Light filters === + === Light Filters === - Once the cuvette holder was finished, '''finding good filters was a tough challenge'''. A main goal throughout our project has been to choose easily available parts which are also inexpensive. Thus choosing Schott glasses as filters unfortunately could not be considered. Instead, filters used for illumination of theaters seemed to be ideal solution. + '''Finding the right and optimal filters is a tough challenge'''. + The main goal throughout our project has been to choose easily available parts which are also inexpensive. Thus choosing Schott glasses as filters could not be considered. Alternatively, filters used for illumination of theaters were found to be an ideal solution. - Especially for the fluorescence measurements of GFP finding the right filter has been a big problem. [http://parts.igem.org/Part:BBa_E0040 GFPmut3b] has a peak excitation at 501 nm and a peak emission at 511 nm - too close together for our low-cost filters to block the excitation light but transmit the emitted light. Thus, we chose to excite at around 485 nm reduce false positive results below 500 nm. However, no adequate filter for these settings could be found. + We tested serveral filters and the optimal configuration of filters used is listed below. - Eventually, using the dark greenish Twickenham Green filter only little amounts of light shorter than 500 nm got through, reducing any bias from excitation illumination significantly. Unfortunately, the transmission rate of this filter is quite bad, 20 % only, for the target emission wavelength of 511 nm. + - For the OD measurement, too, we had similar problems. The solution to this problem is presented in the F device section. + {| class="wikitable" - + ! Mode - + ! Fluorescence Protein - 1. Quite a good random number generator from a computer-scientific perspective! + ! Filter Name - + ! Filter - + ! Peak Excitation - == Combined Device == + ! Peak Emission - + |- - Even though evaluation of the measurements have been performed in two separate device, it is fairly well possible to put everything into one casing. + | Fluorescence - All you need to do is choosing another lid, and connect a second light to frequency sensor to your Arduino. + | [http://parts.igem.org/Part:BBa_E0040 GFPmut3b] - Right at the bottom we present you the differences in wiring things up. + | [http://leefilters.com/lighting/colour-details.html#736 Twickenham Green] - + | [[File:Aachen_Filter_736.png|200px]] - {{Team:Aachen/BlockSeparator}} + | 501nm + | 511nm + |- + | Optical Density + | -- + | [http://leefilters.com/lighting/colour-details.html#019 Fire] + | [[File:Aachen_Filter_019.png|200px]] + | 600nm + | 600nm + |} - = Linearity = + The fluorescence protein [http://parts.igem.org/Part:BBa_E0040 GFPmut3b] has a peak excitation at 501 nm and a peak emission at 511 nm - too close together for our low-cost filters to block the excitation light but transmit the emitted light. Thus, we chose to excite at around 485 nm reduce false positive results below 500 nm. However, no adequate filter for these settings could be found. - As for any scientifc device it is crucial to question the results one gets from the device. To ensure that our device actually works, we performed a set of measurements which are presented below. + Eventually, using the dark greenish [http://leefilters.com/lighting/colour-details.html#736 Twickenham Green] filter only little amounts of light shorter than 500 nm gets through, reducing any bias from excitation illumination significantly. Unfortunately, the transmission rate of this filter is quite bad, 20% only, for the target emission wavelength of 511 nm. + == Linearity of the Hardware Light Sensor == + It is crucial that the selected hardware is mapping reality into the digital world of our $\mu$-Controller. It is crucial that the selected hardware is mapping reality into the digital world of our $\mu$-Controller. In order to sense reality our setup uses a light to frequency sensor, [https://www.sparkfun.com/datasheets/Sensors/Imaging/TSL235R-LF.pdf TSL235R-LF]. In order to sense reality our setup uses a light to frequency sensor, [https://www.sparkfun.com/datasheets/Sensors/Imaging/TSL235R-LF.pdf TSL235R-LF]. Line 61: Line 121: Additionally counting a frequency using interrupts seems to be easier and more accurate than using the analog to digital converter. Additionally counting a frequency using interrupts seems to be easier and more accurate than using the analog to digital converter. - Using a dilution series of purified [ iLOV] we could determine the characteristic curve for the light sensor. Finally we can conclude that the sensor is linear as expected and shown in the [https://www.sparkfun.com/datasheets/Sensors/Imaging/TSL235R-LF.pdf datasheet]. + Using a dilution series of purified [http://2011.igem.org/Team:Glasgow/LOV2 iLOV] we could determine the characteristic curve for the light sensor. Finally we can conclude that the sensor is linear as expected and shown in the [https://www.sparkfun.com/datasheets/Sensors/Imaging/TSL235R-LF.pdf datasheet]. -
+ {{Team:Aachen/Figure|align=center|Aachen 15-10-14 Linearity iFG.PNG|title=Linearity of TSL235R-LF sensor|subtitle=Dilution series of GFP expressing ''E. coli'' showing linearity  between fluorescence count and dilution. The linearity of the chosen sensor can be determined.|width=700px}} - {{Team:Aachen/Figure|align=center|Interlabstudy_overview_wiki.png|title=Interlab Study Results|subtitle=Our measurements of fluorescence and optical density of the three genetic devices and a negative control.|width=1000px}} + - {{Team:Aachen/BlockSeparator}} + -
+ - = OD device = + We are measuring optical density using our in-house developed cuvette holder. + Particularly for optical density measurement, the amount of light shining through the sample is crucial. + If there is too few light, there will be not enough light registered at the sensor, and the resolution of the measurement shrinks. This should be prevented. + The chosen light to frequency sensor is reported to be very sensitive on the amount of light shining on it. + There are reports of the sensor breaking when put into [https://www.sparkfun.com/products/9768 sunlight on a nice day], and not being sensitive at both high light or low light [http://kesslerarduino.wordpress.com/author/kevinmkessler/page/2/ conditions]. - {{Team:Aachen/Figure|Aachen 14-10-09 Flowsheet OD-device ipo.png|title=How to use our OD/F device|subtitle=XXX|width=1000px}} + {{Team:Aachen/BlockSeparator}} + [[File:Aachen_Cuvette_button_v1_ipo.png|right|150px]] + = Evaluation of the Optical Density Measurement = + - + === From Transmittance to True Optical Density === - == From Transmittance to True Optical Density == + At very low levels, uncorrected photometric determinations of cell densities show a decreasing proportionaility to actual cell density. At very low levels, uncorrected photometric determinations of cell densities show a decreasing proportionaility to actual cell density. - This can also be observed using our OD measurement device. + This can also be observed using our device. - In general, photometric determination of bacterial concentrations depends primarily on light scattering, rather than light absorption. Therefore. often not absorption is measured, but transmittance. For this, the relationship between optical density (OD) and transmitted light $\frac{I_0}{I}$ exists as: + In general, photometric determination of bacterial concentrations depends primarily on light scattering, rather than light absorption. Therefore, often not absorption is measured, but transmittance. For this, the relationship between optical density (OD) and transmitted light $\frac{I_0}{I}$ exists as: $$OD = \frac{I_0}{I} = \kappa \cdot c$$ $$OD = \frac{I_0}{I} = \kappa \cdot c$$ + + where $I_0$ is the intensity of incoming light and $I$ the amount of the light passing through. However, this equation is linear only in a certain range. However, this equation is linear only in a certain range. Line 88: Line 153: For our OD device we needed to correlate the transmittance measured by our sensor to an optical density anyway. For our OD device we needed to correlate the transmittance measured by our sensor to an optical density anyway. - Our team members from the deterministic sciences emphasized on the correction method, which was conducted according to Lawrence and Maier [1]: + Our team members from the deterministic sciences emphasized on the correction method, which was conducted according to Lawrence and Maier (2006): * The relative density ($RD$) of each sample in a dilution series is calculated using $\frac{min(dilution)}{dilution}$. * The relative density ($RD$) of each sample in a dilution series is calculated using $\frac{min(dilution)}{dilution}$. Line 97: Line 162: The derived function allows the conversion from transmission to optical density on our device and therefore calibrates our device. The derived function allows the conversion from transmission to optical density on our device and therefore calibrates our device. - Lawrence and Maier could show that correcting transmittance this way, the corrected optical density shows a linear relationship between true optical density and dry weight in cell suspensions. - In our experiments, we find that different cell types have a different correction function. + In our experiments, we find in accordance to Lawrence and Maier that the correction majorly depends on the technical equipment used, especially the LED, sensor and cuvettes. - While this at first sight looks disappointing, it should be expected: + While this at first sight looks disappointing, it is also expected: - Transmittance is the fraction of light coming through some medium relative to the cell-free and clear medium. + Transmittance is the fraction of light not absorbed by some medium relative to the cell-free and clear medium. - However, the transmittance is not only depedent on the amount of cells in the way of the light beam but also on the cells' shape, their size and possibly also their cell membranes. + However, the transmittance is not only dependent on the amount of cells in the way of the light's beam, but also how much light shines through the cuvette in which fashion, and in which fraction is received by the sensor in which angles. - [1] Correction for the Inherent Error in Optical Density Readings, Lawrence, J.V. and Maier, S., Applied and Environmental Microbiology, 1977, p. 482-484 + Using the above formula we performed this experiment for ''Pseudomonas putida'' and ''Saccharomyces cerevisiae'' and asked team [http://2014.igem.org/Team:Aachen/Collaborations/Freiburg Freiburg] to perform the same experiment using mamallian cells. - == DIY: How to Build Your Own OD Device== + === Experiments === - {{Team:Aachen/Figure|Aachen ODdevice Steckplatine.png|align=center|title=Breadboard of our OD device|subtitle=To build your own OD device, connect the parts as shown in this diagram.|width=900px}} + We performed several experiments during the development of the device. + Finally, we can relate the measured transmittance to the true Optical Density (true OD), and further, we can relate the true OD to the true OD of the photospectrometer in our lab. + By doing so, we can calibrate our device to meaningful values. + + We have done this according to the previous section for ''Pseudomonas putida'' and ''Saccharomyces cerevisiae''. + + The final function for calculating the OD from the transmission calculated by our device can be calculated as + + $$OD(T) = f(T) \circ g(device)$$ + + where $f$ transforms transforms transmittance $T$ to true optical density for our device, and $g$ transforms true optical density of our device into the true optical density of the photospectrometer. This way our device is calibrated according to the photospectrometer. + + ==== ''Pseudomonas putida'' ==== + + {{Team:Aachen/Figure|align=center|Aachen 15-10-14 Pputida iFG.PNG|title=True Optical Density to Transmittance plot for ''P. putida''|subtitle=|width=700px}} + + +
+ {{Team:Aachen/Figure|align=center|Aachen 15-10-14 Pputida OD iFG.PNG|title=Corrolating the true optical density of the OD/F Device to true optical density of the photospectrometer for ''P. putida''|subtitle=|width=700px}} +
+ + ==== ''Saccharomyces cerevisiae'' ==== + +
+ {{Team:Aachen/Figure|align=center|Aachen 15-10-14 Scer iFG.PNG|title=True Optical Density to Transmittance plot for ''S. cerivisiae''|subtitle=|width=700px}} +
+ +
+ {{Team:Aachen/Figure|align=center|Aachen 15-10-14 Scer OD iFG.PNG|title=Corrolating the true optical density of the OD/F Device to true optical density of the photospectrometer for ''S. cerivisiae''|subtitle=|width=700px}} +
+ + From these plots, it can be seen that our device delivers robust and reproducible results for both procaryotes and eucaryotes. + Also the function from transmittance to true OD follows a clear pattern, making its calculation possible on a low-end device like a microcontroller. + + It is interesting to observer that function $g$, mapping the true OD of our device to the true OD of the photospectrometer, are close together for both ''P. putida'' and ''S. cerivisae'', as seen by the regression coefficient. + In fact, 3.416 and 3.461 are such close together, that the minor deviation could be just measuring inaccuracy. + Therefore, we fix the regression coefficient for converting true OD of our device to true OD of the photospectrometer to an average of 3.432 . + + Additionally, the function $f$ for mapping transmittance to true OD for our device is similar for all cell types, as seen in the following figure. Therefore the exponential regression curve for all cell types specifies this function. + +
+ {{Team:Aachen/Figure|Aachen_ODallstrains1.png|title=Transmission of different cell types at OD-values from 0.001-1|subtitle=The transmittance data of NIH 3T3 cells (mouse fibroblasts) align with the transmittance of ''P. putida'' and ''S. cerevisiae'' strains, even though the measured optical densities are lower by 1-2 orders of magnitude.|width=800px}} +
+ Finally, we have empirically determined our $OD(T)$ function by finding $f$ and $g$, such that we can convert true OD to the optical density of the photospectrometer. + + By this evaluation, we have shown that our self-build OD/F Device can compete with commercial systems. + It is easy to calibrate by just calculating the true optical density. - If you want to build our OD device, make sure to use the following secret ingredients: - * Filter: [http://www.leefilters.com/lighting/colour-details.html#019 Fire 019] - * LED: {{Team:Aachen/BlockSeparator}} {{Team:Aachen/BlockSeparator}} - = F device = + [[File:Aachen_17-10-14_Glowing_cuvette-ipo.png|right|150px]] - Similarly to the OD measurement, the fluorescence is measured using the same cuvette holder. In fact, if one does not build a combined device, the only thing one is supposed to change is the cuvette holder. + = Evaluation of the Fluorescence Measurement = - However, as for optical density measurement, a filter needs to be placed between led, sample and the light sensor. + - Selecting the filter has been troublesome. + - Either the tried filters had a good transmittance but did not screen for the correct wavelength, or they screened for the correct wavelength but showed bad transmittance. + - Finally we chose the [ Twickenham green] filter with bad transmittance, and raised the sampling interval from 1 s to 4 s to allow a distinct signal. + - This is by far not optimal, but delivers stable and reliable results. + - For fluorescence measurement we luckily are not that much relying on the optical density of the cell culture to measure (if the sample contains cells at all). + For the evaluation of the fluorescence measurement, we performed a dilution series of a constitutively GFPmut3b expressing ''E. coli''. - We compared the values of our device against the [Team:Aachen/LabDevices#platereader platereader]. + - == Evaluation == + The below figure shows the absolute measurements for both the platereader and our OD/F Device. The abrupt jump at 50% concentration can be explained by a second dilution step and is prevalent in both devices. - Figure 1 shows the absolute measurements for both the platereader and our OD/F device. The abrupt jump at 50% concentration can be explained by a second dilution step and is prevalent in both devices. + It can be seen that the platereader show a much higher difference between the GFP and non-GFP cell culture at a higher standard deviation. It can be seen that the platereader show a much higher difference between the GFP and non-GFP cell culture at a higher standard deviation. Another interesting metric is the difference between the GFP and non-GFP, which can be seen as the normalized fluorescence measure. Another interesting metric is the difference between the GFP and non-GFP, which can be seen as the normalized fluorescence measure. - If one compares the results there, as in Figure 2, interesting observations can be made. +
- First, both platereader and OD/F device show very similar results. + {{Team:Aachen/Figure|align=center|Aachn 15-10-14 F platereader ODF iFG.PNG|title=Fluorescence Measurement comparison OD/F Device and Platereader (absolute values)|subtitle=Comparison of a fluorescence measurement of our device and the platereader. Our OD/F Device shows no significant linearity.|width=700px}} +
+ + If one compares the results there, as in the below figure with normalized fluorescence values, interesting observations can be made. + First, both platereader and OD/F Device show very similar results. The regression curves differ only in a linear factor. The regression curves differ only in a linear factor. - Most interestingly general fit of the OD/F device to a linear function seems to be better than with the platereader. + Most interestingly the general fit of the OD/F Device to a linear function seems to be better than the platereader. Overall the linearity which has been observed earlier (in testing the general setup) could be verified. Overall the linearity which has been observed earlier (in testing the general setup) could be verified. - Therefore our do-it-yourself OD/F device can be used to determine fluorescence. + Therefore our do-it-yourself OD/F Device can be used to determine fluorescence. +
+ {{Team:Aachen/Figure|align=center|Aachen 15-10-14 F platereader ODF2 iFG.PNG|title=Fluorescence Measurement comparison OD/F Device and platereader using normalized fluorescence values|subtitle=Comparison of a fluorescence measurement of our device and the platereader. Our OD/F Device shows no significant. A non-GFP expressing ''E. coli'' dilution has been used to normalize the GFP dilution series. A linear correlation can be seen.|width=700px}} +
- === Hint: Building it === - - {{Team:Aachen/Figure|Aachen_Fdevice_Steckplatine.png|align=center|title=Our novel biosensor approach|subtitle=Expression of the TEV protease is induced by HSL. The protease cleaves the GFP-REACh fusion protein to elecit a fluorescence response.|width=900px}} - If you want to build the OD device, make sure to use the following secret ingredients: - * Filter: [http://www.leefilters.com/lighting/colour-details.html#736 Twickenham Green 736] - * LED: {{Team:Aachen/BlockSeparator}} {{Team:Aachen/BlockSeparator}} - = Economical View = + [[File:Aachen_14-10-15_DIY_Cellocks_iNB.png|right|150px]] - + - TODO: + - * what does the market offer, what does the market not offer + - * what is the closest available device to ours and what does it cost? where is it possibly better? where is ours better? + - * how easy is it to get the parts? + + = DIY: How to Build Your Own Device = + + == Technical Components == - Table 2: Needed number of pieces, components and prices for creating your own OD or F device + While the casing and the cuvette holder are custom made, most of the parts are pre-made and can be readily bought. The previous section lists all needed parts. + To get all these parts for creating your own OD/F Device is easy using the internet. Thus all '''potential customers have a market access''' to the used components. + + Please find our custom parts for download below. Despite being custom parts, these are quite inenxpensive - so feel free to give our OD/F Device a test! For printing the 3D model of our cuvette holder and laser cutting our case, we want to express many thanks to [http://hci.rwth-aachen.de/fablab Fablab Aachen]. + + * cuvette holder [http://2014.igem.org/Template:Team:Aachen/cuvette.stl?action=raw STL file] + * casing single device [http://2014.igem.org/wiki/images/b/bb/Aachen_ODF_device_casing.svg.zip SVG file] + * lid combined device [http://2014.igem.org/wiki/images/4/46/Aachen_Odf_device_combined_lid.svg.zip SVG file] + * Arduino Code for single device [http://2014.igem.org/wiki/images/2/2f/Arduino_od_f_single.zip Sketchbook (.ino)] + * Arduino Code for combined device [http://2014.igem.org/wiki/images/e/e8/Arduino_odf_combined.zip Sketchbook (.ino)] + + You will need a special [http://www.exp-tech.de/images/product_images/description%20images/YWRobot/1602/LiquidCrystal_I2C1602V2.rar library] for the display, which can not be uploaded for legal reasons. + + +
+ '''All needed components their quantities and prices for creating your own OD/F Device''' {| class="wikitable" {| class="wikitable" - ! number of pieces !! components !! costs [] + ! align="center" |'''OD/F Device''' + !! align="center" | + !! align="center" |''' 1€=''' + !! align="center" |'''1.27''' + !! align="center" |''' on 14/10/2014''' + !! align="center" | |- |- - | 1|| [http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600#.VDfbWhY2KBk arduino UNO R3]||style="text-align:right" |11.65 + ! Quantity!!Component!! Costs [€] !! Costs [$] !! Final [€] !! Final [$] |- |- - | 1|| [http://www.newark.com/ams/tsl235r-lf/light-to-frequency-converter/dp/06M3670 light to frequency converter TSL 235R]||style="text-align:right" |5.71 + | 1||[http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600#.VDzwV9ysWBp Arduino UNO R3]||9.17||11.65||9.17||11.65 |- |- - | 1|| [http://www.dx.com/p/16-x-2-character-lcd-display-module-with-blue-backlight-121356#.VDfhkxY2KBk display 2x16]||style="text-align:right" |3.28 + | 1||[http://www.mouser.de/ProductDetail/ams/TSL235R-LF/?qs=14HO7rLZPQsjmBHaoYCzkA%3D%3D TSL 235R]||2.47||3.14||2.47||3.14 |- |- - | 1|| [http://www.dx.com/p/lcd1602-adapter-board-w-iic-i2c-interface-black-works-with-official-arduino-boards-216865#.VDrJL9ysWBo LCD display to I2C]||style="text-align:right" | 1.99 + | 1||[http://www.dx.com/p/16-x-2-character-lcd-display-module-with-blue-backlight-121356 Display 16x2]||2.58||3.28||2.58||3.28 |- |- - | 1||LED ([http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== 600 nm] for OD or [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html 480 nm] for F (but any LED should do))||style="text-align:right" |~0.20 + | 1||[http://www.dx.com/p/lcd1602-adapter-board-w-iic-i2c-interface-black-works-with-official-arduino-boards-216865#.VDzxHNysWBp LCD Display to I2C]||1.57||1.99||1.57||1.99 |- |- - | 1||[http://www.newark.com/multicomp/mcpas6b1m1ce3/switch-pushbutton-spst-400ma-125v/dp/12P7696?ost=1638329 pushbutton]||style="text-align:right" |5.23 + | 1||[http://www.newark.com/multicomp/mcpas6b1m1ce3/switch-pushbutton-spst-400ma-125v/dp/12P7696?ost=1638329 Pushbutton]||2.90||3.69||2.90||3.69 |- |- - | 1||[http://shop.leefiltersusa.com/Swatch-Book-Designers-Edition-SWB.htm filter slide]||style="text-align:right" |2 + | 1||[http://shop.leefiltersusa.com/Swatch-Book-Designers-Edition-SWB.htm filter leaflet]||1.57||2.00||1.57||2.00 |- |- - | 20|| [http://www.dx.com/p/diy-male-to-female-dupont-breadboard-jumper-wires-black-multi-color-40-pcs-10cm-339078#.VDgHqBY2KBk jumper-wire-cable]||style="text-align:right" |2.28 + | 20||[http://www.dx.com/p/diy-male-to-female-dupont-breadboard-jumper-wires-black-multi-color-40-pcs-10cm-339078#.VDzxSdysWBp jumper wire cables]||0.09||0.11||1.80||2.28 |- |- - | 1|| [http://www.newark.com/adafruit-industries/65/tiny-breadboard-prototype-electronics/dp/52W9088 small breadboard]||style="text-align:right" |4.00 + | 1||[http://www.dx.com/p/syb-170-mini-breadboard-for-diy-project-red-140101#.VDzyudysWBo small breadboard]||1.98||2.51||1.98||2.51 |- |- - | 1||[http://www.amazon.com/Motorola-Micro-USB-Home-Travel-Charger/dp/B004EYSKM8/ref=sr_1_41?s=wireless&ie=UTF8&qid=1413139568&sr=1-41&keywords=5V+usb+power+supply power supply]||style="text-align:right" |5.00 + | 1||[http://www.dx.com/p/universal-ac-charger-w-dual-usb-output-for-iphone-ipad-ipod-white-us-plug-244893 power supply]||2.20||2.80||2.20||2.80 |- |- - | 1 ||case||style="text-align:right" |20.24 + | 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18 |- |- - | 1|| [http://www.trinckle.com/en/index.php cuvettes-holder]||style="text-align:right" |7.99 + | 1||3 mm acrylic glas (black)||7.98||10.14||7.98||10.14 |- |- - | -||odds and ends like header sockt/pins||style="text-align:right" |2.52 + | 1||[http://www.dx.com/p/prototype-universal-printed-circuit-board-breadboard-golden-10-piece-pack-143913 Prototype Universal Printed Circuit Board]||2.27||2.88||2.27||2.88 + |- + | 1||[http://www.dx.com/p/2-54mm-1x40-pin-breakaway-straight-male-header-10-piece-pack-144191#.VEGRF2d_tGg Male Headers]||2.14||2.72||2.14||2.72 + |- style="border-top: 2px solid #808080;" + | 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600 nm]||0.94||1.19||0.94||1.19 + |- + ! -!!Total OD!!-!!-!! 46.01 !! 58.45 + |- + | 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480 nm]||0.99||1.26||0.99||1.26 + |- + ! -!!Total F!!-!!-!! 46.06 !! 58.52 + |- style="border-top: 2px solid #808080;;" + | 1||[http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== LED 600nm]||0.94||1.19||0.94||1.19 + |- + | 1||[http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html LED 480 nm]||0.99||1.26||0.99||1.26 + |- + | 1||cuvette holder (3D print service of your choice)||6.44||8.18||6.44||8.18 + |- + ! -!!Total OD/F!!-!!-!! 53.44 !! 67.89 |- |- - | -||total||style="text-align:right" |85.16 |} |} +
+ For more detailed economical information about the OD/F project visit our [http://2014.igem.org/Team:Aachen/PolicyPractices/Economics Economical View] page. + == Breadboards == - {{Team:Aachen/BlockSeparator}} + === Optical Density === - = Building your own OD/F device = + {{Team:Aachen/Figure|Aachen ODdevice Steckplatine.png|align=center|title=Breadboard of our OD device|subtitle=To build your own OD device, connect the parts as shown in this diagram.|width=900px}} - While the casing and the cuvette holder are custom made, most of the parts are pre-made and only need to be bought. The previous section [http://2014.igem.org/Team:Aachen/OD/F_device#economicalview Economical View] lists all needed parts. + If you want to build our OD device, make sure to use the following secret ingredients: + * Filter: [http://www.leefilters.com/lighting/colour-details.html#019 Fire 019] + * LED: [http://www.mouser.de/ProductDetail/Dialight/550-2505F/?qs=0KZIkTEbAAvqMAW7suDOXg== 600 nm] Dialight 550-2505F - Please find our custom parts for download below[[http://2014.igem.org/wiki/index.php?title=Team:Aachen/OD/F_device#fn2 1]]. Despite being custom parts, these are quite inenxpensive - so feel free to give our OD/F device a test :) ! + === Fluorescence === - * cuvette holder [http://2014.igem.org/Template:Team:Aachen/cuvette.stl?action=raw STL file] + {{Team:Aachen/Figure|Aachen_Fdevice_Steckplatine.png|align=center|title=Our novel biosensor approach|subtitle=Expression of the TEV protease is induced by HSL. The protease cleaves the GFP-REACh fusion protein to elecit a fluorescence response.|width=900px}} - * casing single device [ SVG file] + If you want to build the OD device, make sure to use the following secret ingredients: - * casing combined device [ SVG file] + * Filter: [http://www.leefilters.com/lighting/colour-details.html#736 Twickenham Green 736] - * Arduino Code for single device [http://2014.igem.org/Template:Team:Aachen/arduino_single.ino?action=raw Sketchbook (.ino)] + * LED:  [http://www.leds.de/Low-Mid-Power-LEDs/SuperFlux-LEDs/Nichia-Superflux-LED-blau-3lm-100-NSPBR70BSS.html 480 nm] NSPBR70BSS LED - * Arduino Code for combined device [http://2014.igem.org/Template:Team:Aachen/arduino_combined.ino?action=raw Sketchbook (.ino)] + - You will need a special [http://www.exp-tech.de/images/product_images/description%20images/YWRobot/1602/LiquidCrystal_I2C1602V2.rar library] for the display, which can not be uploaded for legal reasons. + === Combined Device === + Even though evaluation of the measurements have been performed in two separate device, it is fairly well possible to put everything into one casing. + All you need to do is choosing another lid, and connect a second light to frequency sensor to your Arduino. + Right at the bottom we present you the differences in wiring things up. + Building the combined device is straight forward and very similar to the single device. You will need a slightly larger connector, a different lid for your case, and some more cables. The corresponding fritzing-layout is presented below. - == Build you own device == + {{Team:Aachen/Figure|Aachen_ODF_combined_Steckplatine.png|align=center|title=Our novel biosensor approach|subtitle=Expression of the TEV protease is induced by HSL. The protease cleaves the GFP-REACh fusion protein to elecit a fluorescence response.|width=900px}} + == Construction Steps == {| class="wikitable centered" {| class="wikitable centered" |- |- Line 221: Line 367: | [[File:Aachen_ODF_3.JPG|300px]] || Your lid finally should look like this. | [[File:Aachen_ODF_3.JPG|300px]] || Your lid finally should look like this. |- |- - | [[File:Aachen_ODF_11.JPG|150px]][[File:Aachen_ODF_10.JPG|150px]] || Next we want to assemble the cuvette holders. On the side with the square hole attach the light-to-frequency sensor with glue. For the OD case place the orange LED opposite, or for fluorescence, the LED in the hole in the bottom. Make sure to close any remaining open hole! + | [[File:Aachen_ODF_11.JPG|150px]][[File:Aachen_ODF_10.JPG|150px]] || Next we want to assemble the cuvette holders. On the side with the square hole attach the light-to-frequency sensor with glue. For the OD case place the orange LED opposite, or for fluorescence, the LED in the hole in the bottom. Make sure to close any remaining open hole! Please attach a piece of filter foil (approx. $7 \times 7 mm^2$) from the inside in front of the light to frequency converter. Forceps is highly recommended. |- |- | [[File:Aachen_ODF_12.JPG|300px]] || Your final assembly should then look like this. Now place the correct filter into the cuvette holder, directly in front of the sensor. Make sure that the filter does not degrade due to the glue! | [[File:Aachen_ODF_12.JPG|300px]] || Your final assembly should then look like this. Now place the correct filter into the cuvette holder, directly in front of the sensor. Make sure that the filter does not degrade due to the glue! |- |- - | [[File:Aachen_ODF_14.JPG|300px]] || As the case can be used for both, fluorescence and OD measurement, we use a combined plug. Just three header rows (7 pins) and connect them as we did. + | [[File:Aachen_ODF_14.JPG|300px]] || As the case can be used for both, fluorescence and OD measurement, we use a combined plug. Just three header rows (7 pins, 9pins for combined) and connect them as we did. |- |- | [[File:Aachen_ODF_1.JPG|300px]] || Now we're doing the wiring. Connect the Arduino 5V and GND such that you have one 5V and one GND line on your breadboard. | [[File:Aachen_ODF_1.JPG|300px]] || Now we're doing the wiring. Connect the Arduino 5V and GND such that you have one 5V and one GND line on your breadboard. Line 235: Line 381: | [[File:Aachen_ODF_6.JPG|300px]] || ... also place the cuvette holder into the device. Attach the display to the device lid and close the casing. | [[File:Aachen_ODF_6.JPG|300px]] || ... also place the cuvette holder into the device. Attach the display to the device lid and close the casing. |- |- - | [[File:Aachen_ODF_7.JPG|300px]] || Congratulations! You have finished constructing your own OD/F device! + | [[File:Aachen_ODF_7.JPG|300px]] || Congratulations! You have finished constructing your own OD/F Device! + |- + | [[File:Aachen_zwei_Kuevetten.jpg|300px]] || ... or even the combined device! |} |} - + - 1. iGEM really does not make it easy to distribute non-common files! + - + {{Team:Aachen/BlockSeparator}} {{Team:Aachen/BlockSeparator}} - == Building the combined device == + == References == - + Lawrence, J. V., & Maier, S. (1977). Correction for the inherent error in optical density readings. Applied and Environmental Microbiology, 33(2), 482–484. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=170707&tool=pmcentrez&rendertype=abstract. - {{Team:Aachen/Figure|Aachen_ODF_combined_Steckplatine.png|align=center|title=Our novel biosensor approach|subtitle=Expression of the TEV protease is induced by HSL. The protease cleaves the GFP-REACh fusion protein to elecit a fluorescence response.|width=900px}} + - + - Table 1: Needed number of pieces, components and costs for building your own OD/F device + - {| class="wikitable" + - ! number of pieces !! components !! style="text-align:right" | costs [] + - |- + - | 1|| [http://www.dx.com/p/uno-r3-development-board-microcontroller-mega328p-atmega16u2-compat-for-arduino-blue-black-215600#.VDfbWhY2KBk arduino UNO R3]||style="text-align:right" |11.65 + - |- + - | 2|| [http://www.newark.com/ams/tsl235r-lf/light-to-frequency-converter/dp/06M3670 light to frequency converter TSL 235R]||style="text-align:right" |10.42 + - |- + - | 1|| [http://www.dx.com/p/16-x-2-character-lcd-display-module-with-blue-backlight-121356#.VDfhkxY2KBk display 2x16]||style="text-align:right" |3.28 + - |- + - | 2||LEDs [http://www.newark.com/avago-technologies/hlmp-c423/led-orange-t-1-3-4-5mm-170mcd/dp/06B2750 600nm] and [http://www.newark.com/cree/c503b-bcs-cv0z0461/led-blue-t-1-3-4-5mm-4-1cd-480nm/dp/04R6675 480 nm]||style="text-align:right" |0.39 + - |- + - | 1||taster||style="text-align:right" |5.23 + - |- + - | 1|| [http://www.prolighting.de/Sprache/en/Englisch.htm filter slide]||style="text-align:right" |5.17 + - |- + - | 20|| [http://www.dx.com/p/diy-male-to-female-dupont-breadboard-jumper-wires-black-multi-color-40-pcs-10cm-339078#.VDgHqBY2KBk jumper-wire-cable]||style="text-align:right" |2.28 + - |- + - | 1|| [http://www.newark.com/adafruit-industries/65/tiny-breadboard-prototype-electronics/dp/52W9088 small breadboard]||style="text-align:right" |4.00 + - |- + - | 1||power supply||style="text-align:right" |5.00 + - |- + - | 1 ||case||style="text-align:right" |20.24 + - |- + - | 2|| [http://www.trinckle.com/en/index.php cuvettes-holder]||style="text-align:right" |15.98 + - |- + - | -||odds and ends like header sockt/pins||style="text-align:right" |2.52 + - |- + - | -||total||style="text-align:right" |86.16 + - |} + - + {{Team:Aachen/Footer}} {{Team:Aachen/Footer}} ## Latest revision as of 03:45, 18 October 2014 # OD/F Device On this page we present the technical details of our OD/F Device. You can skip to specific chapters by clicking on the panels below: # General Considerations Building the OD/F Device has been an interesting task. While this device has been developed mainly by the IT division of our team, we got an immense support from the biologists suffering from color-blindness, yet eager to help selecting the best color filters for the LEDs. The measuring principle and guidelines for this project have already been presented in the project section. Here, details about selecting filters, code and a construction manual are presented. ### Cuvette Holder The essential part of this device is the cuvette holder. In short, we had to overcome a dilemma created by the need for an optimal height for the sensor: • A too low sensor position bears problems with sedimentation as well as light diffraction from the bottom of the cuvette. • The sensor has to be as close as possible to the bottom so that enough light shines through for the fluorescence measurement. As a compromise, we place the sensor at a height of 0.75 cm. It is comparable to one of the standard heights (0.2 cm, 0.8 cm, 1.2 cm) of OD meters. It is important to note that our device works with filling volumens of just 1 mL, which in fact comes close to reality in the lab. The final cuvette holder design is rendered from a stl-file shown below: Cuvette Holder developed for our OD/F Device. ### Light Filters Finding the right and optimal filters is a tough challenge. The main goal throughout our project has been to choose easily available parts which are also inexpensive. Thus choosing Schott glasses as filters could not be considered. Alternatively, filters used for illumination of theaters were found to be an ideal solution. We tested serveral filters and the optimal configuration of filters used is listed below. Mode Fluorescence Protein Filter Name Filter Peak Excitation Peak Emission Fluorescence GFPmut3b Twickenham Green 501nm 511nm Optical Density -- Fire 600nm 600nm The fluorescence protein GFPmut3b has a peak excitation at 501 nm and a peak emission at 511 nm - too close together for our low-cost filters to block the excitation light but transmit the emitted light. Thus, we chose to excite at around 485 nm reduce false positive results below 500 nm. However, no adequate filter for these settings could be found. Eventually, using the dark greenish Twickenham Green filter only little amounts of light shorter than 500 nm gets through, reducing any bias from excitation illumination significantly. Unfortunately, the transmission rate of this filter is quite bad, 20% only, for the target emission wavelength of 511 nm. ## Linearity of the Hardware Light Sensor It is crucial that the selected hardware is mapping reality into the digital world of our\mu$-Controller. In order to sense reality our setup uses a light to frequency sensor, TSL235R-LF. The light to frequency sensor resembles the most to a photo transistor and thus is less sensible to temperature than a light dependant resistor. Additionally counting a frequency using interrupts seems to be easier and more accurate than using the analog to digital converter. Using a dilution series of purified iLOV we could determine the characteristic curve for the light sensor. Finally we can conclude that the sensor is linear as expected and shown in the datasheet. We are measuring optical density using our in-house developed cuvette holder. Particularly for optical density measurement, the amount of light shining through the sample is crucial. If there is too few light, there will be not enough light registered at the sensor, and the resolution of the measurement shrinks. This should be prevented. The chosen light to frequency sensor is reported to be very sensitive on the amount of light shining on it. There are reports of the sensor breaking when put into sunlight on a nice day, and not being sensitive at both high light or low light conditions. # Evaluation of the Optical Density Measurement ### From Transmittance to True Optical Density At very low levels, uncorrected photometric determinations of cell densities show a decreasing proportionaility to actual cell density. This can also be observed using our device. In general, photometric determination of bacterial concentrations depends primarily on light scattering, rather than light absorption. Therefore, often not absorption is measured, but transmittance. For this, the relationship between optical density (OD) and transmitted light$\frac{I_0}{I}$exists as: $$OD = \frac{I_0}{I} = \kappa \cdot c$$ where$I_0$is the intensity of incoming light and$I$the amount of the light passing through. However, this equation is linear only in a certain range. While one can tackle this non-linearity by using dilutions of the culture, correcting the error systematically is another way to overcome this limitation. For our OD device we needed to correlate the transmittance measured by our sensor to an optical density anyway. Our team members from the deterministic sciences emphasized on the correction method, which was conducted according to Lawrence and Maier (2006): • The relative density ($RD$) of each sample in a dilution series is calculated using$\frac{min(dilution)}{dilution}$. • The uncorrected optical density is derived from the transmission T [%]:$OD = 2 - \log T$• Finally, the unit optical density is calculated as$\frac{OD}{TD}$. • The average of the stable unit optical densities is used to calculate the true optical density$ OD_{unit} \cdot RD $. This way, the correlation between transmission and true optical density can be computed. The derived function allows the conversion from transmission to optical density on our device and therefore calibrates our device. In our experiments, we find in accordance to Lawrence and Maier that the correction majorly depends on the technical equipment used, especially the LED, sensor and cuvettes. While this at first sight looks disappointing, it is also expected: Transmittance is the fraction of light not absorbed by some medium relative to the cell-free and clear medium. However, the transmittance is not only dependent on the amount of cells in the way of the light's beam, but also how much light shines through the cuvette in which fashion, and in which fraction is received by the sensor in which angles. Using the above formula we performed this experiment for Pseudomonas putida and Saccharomyces cerevisiae and asked team Freiburg to perform the same experiment using mamallian cells. ### Experiments We performed several experiments during the development of the device. Finally, we can relate the measured transmittance to the true Optical Density (true OD), and further, we can relate the true OD to the true OD of the photospectrometer in our lab. By doing so, we can calibrate our device to meaningful values. We have done this according to the previous section for Pseudomonas putida and Saccharomyces cerevisiae. The final function for calculating the OD from the transmission calculated by our device can be calculated as $$OD(T) = f(T) \circ g(device)$$ where$f$transforms transforms transmittance$T$to true optical density for our device, and$g$transforms true optical density of our device into the true optical density of the photospectrometer. This way our device is calibrated according to the photospectrometer. #### Pseudomonas putida #### Saccharomyces cerevisiae From these plots, it can be seen that our device delivers robust and reproducible results for both procaryotes and eucaryotes. Also the function from transmittance to true OD follows a clear pattern, making its calculation possible on a low-end device like a microcontroller. It is interesting to observer that function$g$, mapping the true OD of our device to the true OD of the photospectrometer, are close together for both P. putida and S. cerivisae, as seen by the regression coefficient. In fact, 3.416 and 3.461 are such close together, that the minor deviation could be just measuring inaccuracy. Therefore, we fix the regression coefficient for converting true OD of our device to true OD of the photospectrometer to an average of 3.432 . Additionally, the function$f$for mapping transmittance to true OD for our device is similar for all cell types, as seen in the following figure. Therefore the exponential regression curve for all cell types specifies this function. Finally, we have empirically determined our$OD(T)$function by finding$f$and$g$, such that we can convert true OD to the optical density of the photospectrometer. By this evaluation, we have shown that our self-build OD/F Device can compete with commercial systems. It is easy to calibrate by just calculating the true optical density. # Evaluation of the Fluorescence Measurement For the evaluation of the fluorescence measurement, we performed a dilution series of a constitutively GFPmut3b expressing E. coli. The below figure shows the absolute measurements for both the platereader and our OD/F Device. The abrupt jump at 50% concentration can be explained by a second dilution step and is prevalent in both devices. It can be seen that the platereader show a much higher difference between the GFP and non-GFP cell culture at a higher standard deviation. Another interesting metric is the difference between the GFP and non-GFP, which can be seen as the normalized fluorescence measure. If one compares the results there, as in the below figure with normalized fluorescence values, interesting observations can be made. First, both platereader and OD/F Device show very similar results. The regression curves differ only in a linear factor. Most interestingly the general fit of the OD/F Device to a linear function seems to be better than the platereader. Overall the linearity which has been observed earlier (in testing the general setup) could be verified. Therefore our do-it-yourself OD/F Device can be used to determine fluorescence. # DIY: How to Build Your Own Device ## Technical Components While the casing and the cuvette holder are custom made, most of the parts are pre-made and can be readily bought. The previous section lists all needed parts. To get all these parts for creating your own OD/F Device is easy using the internet. Thus all potential customers have a market access to the used components. Please find our custom parts for download below. Despite being custom parts, these are quite inenxpensive - so feel free to give our OD/F Device a test! For printing the 3D model of our cuvette holder and laser cutting our case, we want to express many thanks to Fablab Aachen. You will need a special library for the display, which can not be uploaded for legal reasons. All needed components their quantities and prices for creating your own OD/F Device OD/F Device 1€=$1.27 on 14/10/2014
QuantityComponent Costs [€] Costs [$] Final [€] Final [$]
1Arduino UNO R39.1711.659.1711.65
1TSL 235R2.473.142.473.14
1Display 16x22.583.282.583.28
1LCD Display to I2C1.571.991.571.99
1Pushbutton2.903.692.903.69
1filter leaflet1.572.001.572.00
20jumper wire cables0.090.111.802.28
1power supply2.202.802.202.80
1cuvette holder (3D print service of your choice)6.448.186.448.18
13 mm acrylic glas (black)7.9810.147.9810.14
1Prototype Universal Printed Circuit Board2.272.882.272.88
1LED 600 nm0.941.190.941.19
-Total OD-- 46.01 58.45
1LED 480 nm0.991.260.991.26
-Total F-- 46.06 58.52
1LED 600nm0.941.190.941.19
1LED 480 nm0.991.260.991.26
1cuvette holder (3D print service of your choice)6.448.186.448.18
-Total OD/F-- 53.44 67.89

### Optical Density

If you want to build our OD device, make sure to use the following secret ingredients:

### Fluorescence

If you want to build the OD device, make sure to use the following secret ingredients:

### Combined Device

Even though evaluation of the measurements have been performed in two separate device, it is fairly well possible to put everything into one casing. All you need to do is choosing another lid, and connect a second light to frequency sensor to your Arduino. Right at the bottom we present you the differences in wiring things up. Building the combined device is straight forward and very similar to the single device. You will need a slightly larger connector, a different lid for your case, and some more cables. The corresponding fritzing-layout is presented below.

## Construction Steps

 First we want to assemble the casing. Once you have all the cut parts, you can start to assemble them. For cutting, we really recommend using a laser cutter. Attach the cuvette-holder holders such that the cuvette holder is placed directly under the opening hole. Next build the lid of the device. At this stage you can already mount the button. We recommend to glue any parts. Your lid finally should look like this. Next we want to assemble the cuvette holders. On the side with the square hole attach the light-to-frequency sensor with glue. For the OD case place the orange LED opposite, or for fluorescence, the LED in the hole in the bottom. Make sure to close any remaining open hole! Please attach a piece of filter foil (approx. $7 \times 7 mm^2$) from the inside in front of the light to frequency converter. Forceps is highly recommended. Your final assembly should then look like this. Now place the correct filter into the cuvette holder, directly in front of the sensor. Make sure that the filter does not degrade due to the glue! As the case can be used for both, fluorescence and OD measurement, we use a combined plug. Just three header rows (7 pins, 9pins for combined) and connect them as we did. Now we're doing the wiring. Connect the Arduino 5V and GND such that you have one 5V and one GND line on your breadboard. Then connect the button to 5V on the one side, and to GND via a resistor on the other side. Connect this side also to port __ on your Arduino. This will sense the blank. Next connect the display to the Arduino and our connector. See the Fritzing diagram at the bottom for a detailed information. Now put everything into the case and ... ... also place the cuvette holder into the device. Attach the display to the device lid and close the casing. Congratulations! You have finished constructing your own OD/F Device! ... or even the combined device!

## References

Lawrence, J. V., & Maier, S. (1977). Correction for the inherent error in optical density readings. Applied and Environmental Microbiology, 33(2), 482–484. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=170707&tool=pmcentrez&rendertype=abstract.