# Team:Aachen/Notebook/Engineering/ODF

(Difference between revisions)
 Revision as of 12:16, 14 October 2014 (view source)Mjoppich (Talk | contribs) (→Do-It-Yourself: Used Parts)← Older edit Revision as of 12:17, 14 October 2014 (view source)Mjoppich (Talk | contribs) (→Do-It-Yourself: Used Parts)Newer edit → Line 278: Line 278: Table 2: Needed number of pieces, components and prices for creating your own OD or F device Table 2: Needed number of pieces, components and prices for creating your own OD or F device - {| class="wikitable" - ! number of pieces !! components !! 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 - |- - | 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/16-x-2-character-lcd-display-module-with-blue-backlight-121356#.VDfhkxY2KBk display 2x16]||style="text-align:right" |3.28 - |- - | 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||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.newark.com/multicomp/mcpas6b1m1ce3/switch-pushbutton-spst-400ma-125v/dp/12P7696?ost=1638329 pushbutton]||style="text-align:right" |5.23 - |- - | 1||[http://shop.leefiltersusa.com/Swatch-Book-Designers-Edition-SWB.htm filter slide]||style="text-align:right" |2 - |- - | 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||[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 ||case||style="text-align:right" |20.24 - |- - | 1|| [http://www.trinckle.com/en/index.php cuvettes-holder]||style="text-align:right" |7.99 - |- - | -||odds and ends like header sockt/pins||style="text-align:right" |2.52 - |- - | -||total||style="text-align:right" |85.16 - |} - {| class="wikitable" {| class="wikitable" ! align="center" |'''OD/F device''' ! align="center" |'''OD/F device''' ## Revision as of 12:17, 14 October 2014 # OD/F Device On this page we invite you to explore our OD/F device and to learn how you can build your own device! ## Development 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. ### Measuring Principle The measuring principle for both optical density (OD) and fluorescence measurement is depicted below. For OD measurement we shine through the sample with an LED and a fixed width. A filter blocks any other light but 600 nm. This way, the sensor mainly senses the 600 nm light which is needed for OD600 measurement. For fluorescence measurement a similar approach is chosen. The filter again is used to block the exciting light from being sensed. That way only the emitted light from the fluorescence protein is measured. The details about selecting filters, code and a construction manual follows. ### 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: • 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, 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. The final cuvette holder design is rendered from a stl-file shown below: ### 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 an ideal solution. Especially for the fluorescence measurements of GFP finding the right filter has been a big problem. 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. For the OD measurement, too, we had similar problems. Indeed, due to our goal of inexpensive parts, we only filter light below 600 nm. Further filters would lower the base transmittance and result in a loss of resolution which is not tolerable. Finally the red filter Fire permits over 70&nbspr; of the light to the sensor and is thus suited for our purposes. 1. Quite a good random number generator from a computer-scientific perspective! # Linearity 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. 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. # 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. # OD device ## Usage Using the presented device is easy and works as with any other device, too. First you will have to take a blank reference, e.g. pure medium without cells. After placing the cuvette in the device, press the red button to take the blank and take out your blank again. In the following do all your measurements which you would like to do compared to your medium. Again, take the cuvette, fill it with the sample and put it into the device. The measured value will be displayed on the device. Do not press the red button again until you want to take another blank/reference. ## 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 OD measurement 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: $$OD = \frac{I_0}{I} = \kappa \cdot c$$ 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 [1]: • 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. 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 in accordance to [1] 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. [1] Correction for the Inherent Error in Optical Density Readings, Lawrence, J.V. and Maier, S., Applied and Environmental Microbiology, 1977, p. 482-484 ## Evaluation We performed several experiments during the development of the OD/F device. Finally we can relate the measured transmittance to the true Optical Density, and further, we can relate that true OD to the one of the photospectrometer in our lab. By doing to 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 $$OD = f(T) \circ g(device)$$ where$f$transforms transforms transmittance 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 first be seen that our device delivers robust and reproducible results for both procaryotes and eucaryotes. Also the function from transmittance to true od can be expressed as a lower polynomial function, making its calculation easily possible on a low-end device like a microcontroller. Most encouraging is that the function for relating the true OD of our device to the photospectrometer is, as seen by the regression coefficient, close together for both P. putida and S. cerivisae. In fact, 3.4199 and 3.4446 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 3.432 . It is interesting to note, that also the function$f$for the conversion of transmittance to true optical density fit nicely together, as can be seen in the following figure. By this evaluation we have shown that our self-build optical density measurement device can compete with commercial systems, and moreover, is easy to calibrate by just calculating the true optical density. Therefore we present a device which measures accurately and is made of easily available parts at a low cost. ## DIY: How to Build Your Own OD Device If you want to build our OD device, make sure to use the following secret ingredients: The instructions for building your own device can be found here. # F device 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. 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). We compared the values of our device against the [Team:Aachen/LabDevices#platereader platereader]. ## Evaluation 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. 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. 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. At higher concentrations our OD/F device struggles regarding accuracy. However, this is also true for the platereader, but at a lower rate. ### Hint: Building it If you want to build the OD device, make sure to use the following secret ingredients: The instructions for building your own device can be found here. # Do-It-Yourself: Used Parts Table 2: Needed number of pieces, components and prices for creating your own OD or F device OD/F device 1€=$1.27 on 14/10/2014
QuantityComponent Costs € Costs $Final € Final$
1Arduino UNO R3 - € $11.65 9.17 €$11.65
1TSL 235R - € $3.14 2.47 €$3.14
1Display 16x2 - € $3.28 2.58 €$3.28
1LCD Display to I2C - € $1.99 1.57 €$1.99
1Pushbutton - € $3.69 2.90 €$3.69
1filter leaflet - € $2.00 1.57 €$2.00
20jumper wire cables - € $0.11 0.09 €$2.28
1small breadboard - € $2.51 1.98 €$2.51
1power supply - € $2.80 2.20 €$2.80
1cuvette holder (3D print service of your choice) 6.44 € $8.18 6.44 €$8.18
13 mm acrylic glas (black) 7.98 € $10.14 7.98 €$10.14
1Prototype Universal Printed Circuit Board - € $2.88 2.27 €$2.88
1Male Headers - € $2.72 2.14 €$2.72
1LED 600nm 0.99 € $1.11 0.87 €$1.11
Total OD 45.94 € $58.37 1LED 480nm 0.99 €$1.26 0.99 € $1.26 Total F 46.06 €$58.52

# Building your own OD/F device

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 Used Parts lists all needed parts.

Please find our custom parts for download below[1]. Despite being custom parts, these are quite inenxpensive - so feel free to give our OD/F device a test :) !

You will need a special library for the display, which can not be uploaded for legal reasons.

## Build you own device

 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) 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!

1. iGEM really does not make it easy to distribute anything different than default image files!

## Building the combined device

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 maybe more cables. The changed fritzing-layout is presented below.

Table 1: Needed number of pieces, components and costs for building your own OD/F device

number of pieces components costs [\$]
1 arduino UNO R311.65
2 light to frequency converter TSL 235R10.42
1 display 2x163.28
2LEDs 600nm and 480 nm0.39
1taster5.23
1 filter slide5.17
20 jumper-wire-cable2.28