Difference between revisions of "Team:Lambert GA/Software"

 
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<center><h3 style="color: #D49AE6;">Function</h3></center>
 
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<p style="width: 100%; margin: auto; font-size: 16px;">The Chrome-Q Light Chamber is a 3D-printed imaging measurement system used to quantify chromoproteins/color-based data. For our current project, it is used to quickly and inexpensively measure relative protein degradation through quantification of the color in chromoprotein expression.
 
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</p></center>
 
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<div class="center">
 
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<img class="img-responsive" style="width:600px" src="https://static.igem.org/mediawiki/2017/b/b2/T--LambertGA--camera2.jpg">
 
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<center><h3 style="color: #D49AE6;">Development</h3></center>
 
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<p style="width: 100%; margin: auto; font-size: 16px;">One of the most critical variables in imaging today is the consistency of light. Different wavelengths, intensity, power, wattage, and even angling of lights can affect the result of camera imaging. To this end, the Chrome-Q  is designed to control these variables of light. The dimensions and dome shape have been optimized for ideal imaging distance and lighting amount. A parallel circuit was used in order to distribute full and equal voltage to each LED in the Chrome-Q. This flowchart explains our process/iterations.</p><center><img src="https://static.igem.org/mediawiki/2017/archive/7/7d/20171101161027%21T--Lambert_GA--EngineeringProcessChromeQ.png" style="height: 550px;"></center>
 
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<br>
 
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<center><h3 style="color: #D49AE6;">On-Site Application</h3></center>
 
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<p style="width: 100%; margin: auto; font-size: 16px;">To use the Chrome-Q, first a sample must be placed in the wells in the base under the dome. Then, using the app, a phone can take a picture of the sample through the eyehole, and calculate degradation of protein by analyzing the saturation and hue values derived from the RGB values in the pixels of the samples.</p>
 
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<br>
 
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<center><h3 style="color: #D49AE6;">Inexpensive</h3></center>
 
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<p style="width: 100%; margin: auto; font-size: 16px;">As a high school lab, one of the many problems we face in research is the lack of funding and financial support. Sophisticated equipment is incredibly expensive, and so it is very hard to afford or even gain access to the necessary tools and measurement systems for our research, such as plate readers and fluorimeters, that we use to measure our circuits expression. The Chrome-Q Light Chamber is designed to conquer the issue of the cost of a fluorimeter – instead of visualizing with fluorescence, the project uses color and RGB values, which can then be imaged with the chamber we built, and results can be obtained that way. This technology can be used by other teams and facilities for their research, and the full plan of the design is available below so that any team can build it themselves. The materials needs for the Chrome-Q costs around $10 and is easily assembled, while plate readers and fluorimeters can easily cost upwards of $5,000. </p>
 
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<br>
 
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<center><h3 style="color: #D49AE6;">Build Guide</h3></center>
 
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<center><a href="https://static.igem.org/mediawiki/2017/0/05/T--Lambert_GA--Chrome-QFiles.zip"> The files can be found here.</a></center>
 
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<p style="width: 100%; margin: auto; font-size: 16px;">
 
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<b style="font-size: 20px;">Tools</b>
 
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<p style="width: 100%; margin: auto; font-size: 16px;">1. 3D Printer (Build Area of at least 7 x 7 x 8in)
 
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<br>
 
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2. Non-Reflective Spray Paint
 
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<br>
 
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3. Camera </p><br><br>
 
  
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<b style="font-size: 20px;">Parts</b>
 
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<p style="width: 100%; margin: auto; font-size: 16px;">1. All the STL files included within the file.
 
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<br>
 
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2. LED Lights(3, G4 LED Bulb - 2 Watt (20 Watt Equivalent) Bi-Pin LED Disc - White - 170 Lumens - Natural White)
 
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<br>
 
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3. 9-Volt batteries(2)<br>
 
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4. Wire (18-22 gauge, at personal discretion)
 
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<br>
 
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5. 3 Ohm Resistor(2)
 
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</p>
 
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<br><br><br>
 
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<h3 style="color: #D49AE6;"><center>Circuit Design</center></h3>
 
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<center><img src="https://static.igem.org/mediawiki/2017/6/67/T--Lambert_GA--CircuitDesign.png" width="400px;">
 
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<br>
 
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<i style="font-size: 14px; color: white;"> Circuit design layout for the Chrome-Q system </i></center>
 
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<br>
 
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<b>Tips</b>
 
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<p style="width: 100%; margin: auto; font-size: 16px;">For best results, print at a slow speed to ensure the best outcome possible and make sure the 3D printer is tuned correctly. Print each of the Parts at any desired infill percentage and layer height. Also, it’s recommended to print with brims so it does not curl when printing. If need be, the SLDPRT versions are included in the file. Be sure to wire the circuit with the batteries in a daisy-chain, with the resistors placed after the power source. The design will work if powered by a outlet, we used batteries to power the circuit in order to make it easily portable.</p>
 
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<br><br>
 
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<b style="font-size: 20px;">Instructions</b>
 
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<p style="width: 100%; margin: auto; font-size: 16px;">1. Transfer all the STL files into preferred slicing software. <br>
 
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2. Change settings accordingly to the printer. <br>
 
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3. Orient the parts where it can be printed easiest. <br>
 
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4. Convert it into GCODE files. <br>
 
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5. Transfer the GCODE files into preferred printing software. <br>
 
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6. Start Printing.<br>
 
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<p style="width: 100%; margin: auto; font-size: 16px;">7. Carefully remove the prints. <br>
 
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8. Sand any defects <br>
 
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9. Test that the dome fits on base. <br>
 
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10. Build parallel circuit with batteries and LEDs. <br>
 
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11. Align circuit such that LEDs fit into slots. <br>
 
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<b>*Note: If you are interested in 3D-printing the Chrome-Q Light Chamber, please contact us at igem.lamb@gmail.com for the program print files. </b> </p>
 
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<br>
 
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<center> <h2>  References </h2> </center>
 
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<p>Dhakar, L. (n.d.). Image Color Picker (Z. A., Ed.). Retrieved October 10, 2017, from
 
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http://www.colorcodepicker.com/
 
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<br><br>
 
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Purple color codes. (n.d.). Retrieved October 10, 2017, from
 
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http://www.rapidtables.com/web/color/purple-color.htm
 
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<br><br>
 
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RGB Color Gradient Maker. (n.d.). Retrieved October 10, 2017, from http://www.perbang.dk/rgbgradient/
 
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<br><br>
 
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Tamura, K., Shimada, T., Ono, E., Tanaka, Y., Nagatani, A., Higashi, S., . . . Hara-Nishimura, I. (2003,
 
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September). Why green fluorescent fusion proteins have not been observed in the vacuoles of
 
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higher plants. The Plant Journal, 35(4), 545-555. doi:10.1046/j.1365-313X.2003.01822.x
 
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</p>
 
 
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       <a class="drplink" style="transition: color 0.5s ease-in-out;" href="https://2017.igem.org/Team:Lambert_GA/Applied_Design">Applied Design</a>
 
       <a class="drplink" style="transition: color 0.5s ease-in-out;" href="https://2017.igem.org/Team:Lambert_GA/Applied_Design">Applied Design</a>
 
<a class="drplink" style="transition: color 0.5s ease-in-out;" href="https://2017.igem.org/Team:Lambert_GA/Hardware">Hardware</a>
 
<a class="drplink" style="transition: color 0.5s ease-in-out;" href="https://2017.igem.org/Team:Lambert_GA/Hardware">Hardware</a>
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      <a class="drplink" style="transition: color 0.5s ease-in-out;" href="https://2017.igem.org/Team:Lambert_GA/Measurement">Measurement</a>
 
 
       <a class="drplink" style="transition: color 0.5s ease-in-out;" href="https://2017.igem.org/Team:Lambert_GA/Model">Model</a>
 
       <a class="drplink" style="transition: color 0.5s ease-in-out;" href="https://2017.igem.org/Team:Lambert_GA/Model">Model</a>
 
<a class="drplink" style="transition: color 0.5s ease-in-out;" href="https://2017.igem.org/Team:Lambert_GA/Software">Software</a>
 
<a class="drplink" style="transition: color 0.5s ease-in-out;" href="https://2017.igem.org/Team:Lambert_GA/Software">Software</a>
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<center> <h1 id="MainTitle"><b>Software </b></h1><img src="https://static.igem.org/mediawiki/2017/b/bc/T--Lambert_GA--purpleline.png" style="width:18%; margin:auto;"> </center> <br>
 
<center> <h1 id="MainTitle"><b>Software </b></h1><img src="https://static.igem.org/mediawiki/2017/b/bc/T--Lambert_GA--purpleline.png" style="width:18%; margin:auto;"> </center> <br>
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<p style="font-size:20px;">
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<center><h3 style="color: #D49AE6;">Chrome-Q App</h3></center>
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<p style=" font-size: 20px;">Chrome-Q is a Xamarin C# app created in Microsoft Visual Studio 2017 Community Edition. The app was developed for mobile Android devices and will soon be available for iOS devices. A photo is taken (within the app) of the Chrome-Q dome target base (that contains the rows of samples in triplicate). The app finds the samples in the photo by looking for low luminance values compared to the high luminance values in the white background. Then, the app finds the average hue and luminance for each sample by averaging the RGB values for all of the pixels in the circular sample. It groups the samples into rows by comparing their vertical locations in the photo. After grouping into rows, it calculates the average RGB values for the entire row to generate an average hue and luminance for the triplicate. The average hue and luminance are utilized to calculate the standard deviation of the triplicate. By looking at the standard deviation, it was determined that the hue values were most consistent in the triplicate. These values can then be used to compare relative levels of degradation between the different constructs (tsPurple, tsPurpleDAS, and tsPurpleLAA).
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</p>
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<center>
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<br><br>
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<img src="https://static.igem.org/mediawiki/2017/1/1c/Appfindingcircles.jpeg" style="width:450px; margin:auto;">
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<br><br>
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<i style="font-size: 14px; color: white;"> Chromoprotein samples in the Chrome-Q well plate and the Chrome-Q app recognizing the colors (represented by the green dots) </i>
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<br><br>
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<img src="https://static.igem.org/mediawiki/2017/b/bb/Newtspurplechart.png" style="width:450px; margin:auto;">
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<br><br>
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<i style="font-size: 14px; color: white;"> Data gathered on tsPurple samples using the Chrome-Q model and app </i>
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<br><br>
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<img src="https://static.igem.org/mediawiki/2017/1/11/Updatedhuetspurplechart.png" style="width:450px; margin:auto;">
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<br><br>
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<i style="font-size: 14px; color: white;"> The hue values of tsPurple at different levels of IPTG induction </i>
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<br>
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<p style=" font-size: 20px;"> Important Note: Hues values range from 0 to 360 degrees. The hue values in the samples begin at around 270 degrees (purple) and increase through 360 degrees. The hues value 0 uL IPTG concentration wraps around to a low hue value of around 40 degrees. To process these hues, 360 degrees were added to values less than 180 degrees, which is why some values are greater than 360. </p>
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<br><br>
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<img src="https://static.igem.org/mediawiki/2017/a/a0/%25purplechart.png" style="width:450px; margin:auto;">
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<br><br>
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<i style="font-size: 14px; color: white;"> The % purple of tsPurple samples at different levels of IPTG induction </i>
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<br><br>
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<img src="https://static.igem.org/mediawiki/2017/6/62/Notjankychromeqpic.jpeg" style="width:450px; margin:auto;">
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<br><br>
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<i style="font-size: 14px; color: white;"> Team member Emily Gibson using the Chrome-Q system </i>
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<br><br><br>
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<center> <h2>  References </h2> </center>
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<p>Dhakar, L. (n.d.). Image Color Picker (Z. A., Ed.). Retrieved October 10, 2017, from
 +
http://www.colorcodepicker.com/
 +
<br><br>
 +
Purple color codes. (n.d.). Retrieved October 10, 2017, from
 +
http://www.rapidtables.com/web/color/purple-color.htm
 +
<br><br>
 +
RGB Color Gradient Maker. (n.d.). Retrieved October 10, 2017, from http://www.perbang.dk/rgbgradient/
 +
<br><br>
 +
Tamura, K., Shimada, T., Ono, E., Tanaka, Y., Nagatani, A., Higashi, S., . . . Hara-Nishimura, I. (2003,
 +
September). Why green fluorescent fusion proteins have not been observed in the vacuoles of
 +
higher plants. The Plant Journal, 35(4), 545-555. doi:10.1046/j.1365-313X.2003.01822.x
 +
</p>
 +
 +
 +
</center>
 +
</p>
 
<div id="sponsors-bottom">
 
<div id="sponsors-bottom">
  

Latest revision as of 17:17, 12 December 2017



Software


Chrome-Q App

Chrome-Q is a Xamarin C# app created in Microsoft Visual Studio 2017 Community Edition. The app was developed for mobile Android devices and will soon be available for iOS devices. A photo is taken (within the app) of the Chrome-Q dome target base (that contains the rows of samples in triplicate). The app finds the samples in the photo by looking for low luminance values compared to the high luminance values in the white background. Then, the app finds the average hue and luminance for each sample by averaging the RGB values for all of the pixels in the circular sample. It groups the samples into rows by comparing their vertical locations in the photo. After grouping into rows, it calculates the average RGB values for the entire row to generate an average hue and luminance for the triplicate. The average hue and luminance are utilized to calculate the standard deviation of the triplicate. By looking at the standard deviation, it was determined that the hue values were most consistent in the triplicate. These values can then be used to compare relative levels of degradation between the different constructs (tsPurple, tsPurpleDAS, and tsPurpleLAA).





Chromoprotein samples in the Chrome-Q well plate and the Chrome-Q app recognizing the colors (represented by the green dots)



Data gathered on tsPurple samples using the Chrome-Q model and app



The hue values of tsPurple at different levels of IPTG induction

Important Note: Hues values range from 0 to 360 degrees. The hue values in the samples begin at around 270 degrees (purple) and increase through 360 degrees. The hues value 0 uL IPTG concentration wraps around to a low hue value of around 40 degrees. To process these hues, 360 degrees were added to values less than 180 degrees, which is why some values are greater than 360.





The % purple of tsPurple samples at different levels of IPTG induction



Team member Emily Gibson using the Chrome-Q system


References

Dhakar, L. (n.d.). Image Color Picker (Z. A., Ed.). Retrieved October 10, 2017, from http://www.colorcodepicker.com/

Purple color codes. (n.d.). Retrieved October 10, 2017, from http://www.rapidtables.com/web/color/purple-color.htm

RGB Color Gradient Maker. (n.d.). Retrieved October 10, 2017, from http://www.perbang.dk/rgbgradient/

Tamura, K., Shimada, T., Ono, E., Tanaka, Y., Nagatani, A., Higashi, S., . . . Hara-Nishimura, I. (2003, September). Why green fluorescent fusion proteins have not been observed in the vacuoles of higher plants. The Plant Journal, 35(4), 545-555. doi:10.1046/j.1365-313X.2003.01822.x