Difference between revisions of "Team:York/Hardware"

 
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<div class="column full_size judges-will-not-evaluate">
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<div>
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<h3>★  ALERT! </h3>
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    <!-- Header -->
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<p>This page is used by the judges to evaluate your team for the <a href="https://2017.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2017.igem.org/Judging/Awards"> award listed above</a>. </p>
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    <header class="intro-header" style="background: url(//2017.igem.org/wiki/images/2/27/TeamYork-TemporaryBackground.png); background-size: 100% 100%; background-position:0px 20px;">
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<p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2017.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
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            <div class="intro-message text-center container" style = "margin: 0px 0px;">
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                <br style = “line-height:20px;”><br>
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                <h1 style="-webkit-text-stroke: 2px black; color:#fff;">Hardware</h1>
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                <h1 style="-webkit-text-stroke: 2px black; color:#fff;">Upright DIHM & Analysis Chamber</h1>
 
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<div class="cam-container" style="background-color: #ddd; color: #000;">
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<h1>Hardware</h1>
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<section style="padding-top: 10px; padding-bottom: 20px; margin-top: 0px;">
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<h3>Best Hardware Special Prize</h3>
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  <br>
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<p>iGEM is about making teams of students making synthetic biology projects. We encourage teams to work with parts and build biological devices in the lab. But we are inclusive and want all teams to work on many other types of problems in synbio. Robotic assembly, microfluidics, low cost equipment and measurement hardware are all areas ripe for innovation in synbio. </p>
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  <div class="container" style="background-color: rgb(250,250,250); color: #000000; border-style: solid; border-color: #000000; border-radius: 25px;">
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    <div class="text-center">
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<p>
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      <h1>Upright DIHM</h1>
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Teams who are interested in working with hardware as a side project are encouraged to apply for the hardware award.
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    </div>
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    <div class="text-left" style="margin: 0px;">
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<br><br>
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      <p style="font-size: 18px;">As outlined on the <a style="color: #0000ff;" href="//2017.igem.org/Team:York/Description">Description</a> page, we made our microscope out of an aluminium diecast box, a piece of profile extrusion and some plastic blocks. The designs are available via our Downloads page. Once all the parts are acquired, the following assembly process should be used. We have provided step by step instructions, below.</p>
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To compete for the <a href="https://2017.igem.org/Judging/Awards">Best Hardware prize</a>, please describe your work on this page and also fill out the description on the <a href="https://2017.igem.org/Judging/Judging_Form">judging form</a>.
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    </div>
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<br><br>
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    <br style="line-height: 10px;">
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You must also delete the message box on the top of this page to be eligible for this prize.
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  </div>
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</p>
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</section>
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</p>
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</div>
 
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<div class="cam-container" style="background-color: #ddd; color: #000;">
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<section style="padding-top: 10px; padding-bottom: 20px; margin-top: 0px;">
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<h5>Inspiration</h5>
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  <div class="container" style="background-color: rgba(223,230,239,0.9); color: #162844; border-style: solid; border-color: #162844; border-radius: 25px;">
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<p>You can look at what other teams did to get some inspiration! <br />
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    <div class="text-center">
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Here are a few examples:</p>
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      <h1>Assembly</h1>
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<ul>
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    </div>
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<li><a href="https://2016.igem.org/Team:Valencia_UPV">2016 Valencia UPV</a></li>
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    <div class="text-left" style="margin: 0px;">
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<li><a href="https://2016.igem.org/Team:Aachen">2016 Aachen </a></li>
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      <center>
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<li><a href="https://2015.igem.org/Team:TU_Delft">2015 TU Delft  </a></li>
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        <p style="text-align: center; font-size: 20px;"><strong>Connect the Base and Profile Extrusion</strong><br></p>
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<li><a href="https://2015.igem.org/Team:TU_Darmstadt">2015 TU Darmstadt</a></li>
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                  <div style="border-style: solid; border-color: #162844; border-radius: 25px;">
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                    <img width="100%" style="border-style: solid; border-color: #162844; border-radius: 25px;" src="//2017.igem.org/wiki/images/4/4d/IGEM-York-DIHM-Base.jpg">
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                  </div>
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                </li>
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              </ul>
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          </div>
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                <li><br></li>
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                <li>
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                  <div style="border-style: solid; border-color: #162844; border-radius: 25px;">
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                    <img width="100%" style="border-style: solid; border-color: #162844; border-radius: 25px;" src="//2017.igem.org/wiki/images/b/be/IGEM-York-Profile-Extrusion-End.jpg">
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                  </div>
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                </li>
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              </ul>
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            <center>
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          </div>
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          <div class="col-md-3">
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                  <div style="border-style: solid; border-color: #162844; border-radius: 25px;">
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                    <img width="100%" style="border-style: solid; border-color: #162844; border-radius: 25px;" src="//2017.igem.org/wiki/images/a/ac/IGEM-York-Base-and-Extrusion-Front.jpg">
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                  </div>
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                </li>
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            <center>
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          <div class="col-md-3">
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            <center>
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                  <div style="border-style: solid; border-color: #162844; border-radius: 25px;">
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                    <img width="100%" style="border-style: solid; border-color: #162844; border-radius: 25px;" src="//2017.igem.org/wiki/images/5/54/IGEM-York-Base-and-Extrusion-Back.jpg">
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                  </div>
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                </li>
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              </ul>
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            <center>
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          </div>
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        </div>
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        <p style="font-size: 18px; text-align: center;">Tap the holes in the profile extrusion so that it can be screwed onto the base as shown.</p>
 +
      </center>
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<br><hr><br>
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      <center>
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        <p style="text-align: center; font-size: 20px;"><strong>Prepare the Raspberry Pi</strong><br></p>
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                  <div style="border-style: solid; border-color: #162844; border-radius: 25px;">
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                    <img width="100%" style="border-style: solid; border-color: #162844; border-radius: 25px;" src="//2017.igem.org/wiki/images/e/e1/IGEM-York-Pi-Cam-Hat-Separate.jpg">
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                  </div>
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                </li>
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              </ul>
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            <center>
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          </div>
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                <li><br></li>
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                  <div style="border-style: solid; border-color: #162844; border-radius: 25px;">
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                    <img width="100%" style="border-style: solid; border-color: #162844; border-radius: 25px;" src="//2017.igem.org/wiki/images/a/a0/IGEM-York-Pi-Cam-Together-Hat-Separate.jpg">
 +
                  </div>
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                </li>
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              </ul>
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            <center>
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          <div class="col-md-4">
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                    <img width="100%" style="border-style: solid; border-color: #162844; border-radius: 25px;" src="//2017.igem.org/wiki/images/7/7f/IGEM-York-Pi-Cam-Hat-Together.jpg">
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                  </div>
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                </li>
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              </ul>
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            <center>
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          </div>
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        </div>
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      </center>
 +
      <p style="text-align: center; font-size: 18px;">Connect the Explorer hat PRO and Camera Module V2 to the Raspberry Pi 3 as in the images. Note that we removed the lens from the camera.</p>
 +
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<br><hr><br>
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      <center>
 +
        <p style="text-align: center; font-size: 20px;"><strong>Connect the Raspberry Pi</strong><br></p>
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        <div class="row">
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          <div class="col-md-2"></div>
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          <div class="col-md-4">
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                  <div style="border-style: solid; border-color: #162844; border-radius: 25px;">
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                    <img width="100%" style="border-style: solid; border-color: #162844; border-radius: 25px;" src="//2017.igem.org/wiki/images/9/9d/IGEM-York-Camera-to-Base.jpg">
 +
                  </div>
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                </li>
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              </ul>
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            <center>
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          </div>
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          <div class="col-md-4">
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            <center>
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              <ul style="list-style: none;">
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                <li><br></li>
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                <li>
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                  <div style="border-style: solid; border-color: #162844; border-radius: 25px;">
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                    <img width="100%" style="border-style: solid; border-color: #162844; border-radius: 25px;" src="//2017.igem.org/wiki/images/d/de/IGEM-York-Connect-Power.jpg">
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                  </div>
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          </div>
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          <div class="col-md-2"></div>
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        </div>
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      </center>
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      <p style="text-align: center; font-size: 18px;">Screw the Camera into the position shown using nylon (non-conductive) screws. Connect the power cable to the Pi through the back of the base. This is also where HDMI/USB connections should be made.</p>
 +
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<br><hr><br>
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      <center>
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        <p style="text-align: center; font-size: 20px;"><strong>Build the Circuitry</strong><br></p>
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            <center>
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                  <div style="border-style: solid; border-color: #162844; border-radius: 25px;">
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                    <img width="100%" style="border-style: solid; border-color: #162844; border-radius: 25px;" src="//2017.igem.org/wiki/images/f/f9/IGEM-York-Circuitry.jpg">
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                  </div>
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                </li>
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              </ul>
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            <center>
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                  <div style="background-color: #fff; border-style: solid; border-color: #162844; border-radius: 25px;">
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                    <img width="100%" style="border-style: solid; border-color: #162844; border-radius: 25px;" src="//2017.igem.org/wiki/images/3/33/IGEM-York-CircuitDiagram.png">
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                  </div>
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                </li>
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            <center>
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          </div>
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          <div class="col-md-2">
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          </div>
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        </div>
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        <p style="font-size: 18px; text-align: center;">We used a 635 nm <a style="color: #0000ff;" href="//www.thorlabs.com/thorproduct.cfm?partnumber=L635P5">laser diode</a> and corresponding <a style="color: #0000ff;" href="//www.thorlabs.com/thorproduct.cfm?partnumber=S7060R">socket</a> from Thorlabs. Soldering the socket prevents heat damage to the diode itself. Our variable resistor (potentiometer) had a maximum value of 200 Ω.</p>
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      </center>
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<br><hr><br>
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      <center>
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        <p style="text-align: center; font-size: 20px;"><strong>Connect the Laser</strong><br></p>
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        <div class="row">
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          <div class="col-md-2">
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                  <div style="border-style: solid; border-color: #162844; border-radius: 25px;">
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                    <img width="100%" style="border-style: solid; border-color: #162844; border-radius: 25px;" src="//2017.igem.org/wiki/images/3/3a/IGEM-York-Cable-Feeding.jpg">
 +
                  </div>
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                </li>
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            <center>
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          </div>
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          <div class="col-md-4">
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            <center>
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                <li>
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                  <div style="border-style: solid; border-color: #162844; border-radius: 25px;">
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                    <img width="100%" style="border-style: solid; border-color: #162844; border-radius: 25px;" src="//2017.igem.org/wiki/images/e/eb/IGEM-York-Connect-Laser.jpg">
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                  </div>
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                </li>
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              </ul>
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            <center>
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          </div>
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          <div class="col-md-2">
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          </div>
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        </div>
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        <p style="font-size: 18px; text-align: center;">Feed the wires from the circuitry through the profile extrusion, as shown, then connect the positive to the Explorer Hat's 5V output and negative to ground. At this point, the Pi can be sealed inside the diecast box, by adding the base plate.</p>
 +
        <center>
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          <div class="row">
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            <div class="col-md-3"></div>
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            <div class="col-md-6" style="border-style: solid; border-color: #162844; border-radius: 25px; padding: 0;">
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              <img style="border-style: solid; border-color: #162844; border-radius: 25px;" src="//2017.igem.org/wiki/images/e/ee/IGEM-York-Close-Base.jpg" width="100%">
 +
            </div>
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            <div class="col-md-3"></div>           
 +
          </div>
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        </center>
 +
      </center>
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<br><hr><br>
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      <center>
 +
        <p style="text-align: center; font-size: 20px;"><strong>Add the Platforms</strong><br></p>
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        <div class="row">
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            <center>
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                <li><br></li>
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                <li>
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                  <div style="border-style: solid; border-color: #162844; border-radius: 25px;">
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                    <img width="100%" style="border-style: solid; border-color: #162844; border-radius: 25px;" src="//2017.igem.org/wiki/images/f/f1/IGEM-York-Laser-Platform-Screws.jpg">
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                  </div>
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                </li>
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              </ul>
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            <center>
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          </div>
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          <div class="col-md-3">
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            <center>
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                <li><br></li>
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                <li>
 +
                  <div style="border-style: solid; border-color: #162844; border-radius: 25px;">
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                    <img width="100%" style="border-style: solid; border-color: #162844; border-radius: 25px;" src="//2017.igem.org/wiki/images/5/5f/IGEM-York-Laser-Platform-Screws-Attached.jpg">
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                  </div>
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                </li>
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            <center>
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                  <div style="border-style: solid; border-color: #162844; border-radius: 25px;">
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                    <img width="100%" style="border-style: solid; border-color: #162844; border-radius: 25px;" src="//2017.igem.org/wiki/images/0/06/IGEM-York-Laser-Platform-Screws-Attached-to-Neck.jpg">
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                  </div>
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                </li>
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            <center>
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          </div>
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            <center>
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                  <div style="border-style: solid; border-color: #162844; border-radius: 25px;">
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                    <img width="100%" style="border-style: solid; border-color: #162844; border-radius: 25px;" src="//2017.igem.org/wiki/images/c/c1/IGEM-York-Laser-Platform-in-Place.jpg">
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                  </div>
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        </div>
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        <p style="font-size: 18px; text-align: center;">Attach the screws and fixings to the platform. (We used Item <a style="color: #0000ff;" href="//product.item24.co.uk/en/home/products/product-catalogue/productdetails/products/construction-profiles-5/profile-5-80x20-natural-37086.html">profile extrusion</a>, so we used their <a style="color: #0000ff;" href="//product.item24.co.uk/en/home/products/product-catalogue/productdetails/products/t-slot-nuts-st-1/t-slot-nut-5-st-m5-bright-zinc-plated-37001.html">T-slot nut</a> fixings.) Then, slide each of the platforms into place.</p>
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                    <img width="100%" style="border-style: solid; border-color: #162844; border-radius: 25px;" src="//2017.igem.org/wiki/images/e/e5/IGEM-York-CircuitryCover-Real.jpg">
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                <li><br></li>
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                  <div style="border-style: solid; border-color: #162844; border-radius: 25px;">
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                    <img width="100%" style="border-style: solid; border-color: #162844; border-radius: 25px;" src="//2017.igem.org/wiki/images/d/dc/IGEM-York-CircuitryCover-Top.jpg">
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        <p style="font-size: 18px; text-align: center;">Finally, add the top cover to conceal the circuitry.</p>
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<br><hr><br>
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      <center>
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        <p style="text-align: center; font-size: 40px;"><strong>Congratulations!</strong><br></p>
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                    <img width="100%" style="border-style: solid; border-color: #162844; border-radius: 25px;" src="//2017.igem.org/wiki/images/1/18/IGEM-York-Full-Assembly.jpg">
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          </div>
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        <p style="font-size: 24px; text-align: center;">Well done! You now have an assembled Digital Inline Holographic Microscope!</p>
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      </center>
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    </div>
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    <br style="line-height: 10px;">
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<div class="cam-container" style="background-color: #ddd; color: #000;">
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<a href="https://static.igem.org/mediawiki/2017/d/df/Chlamydomonas-Transformation-Protocol-York-iGEM.pdf">PDF Link</a>
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      <h1>Milli-fluidic Analysis Chamber</h1>
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    <div class="text-left" style="margin: 0px;">
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      <p style="font-size: 18px;">We have written a protocol detailing the assembly of both iterations of our milli-fluidic chamber. One uses PDMS and the other uses poly-acryl to form the chamber itself while both make use of glass slides.</p>
 +
      <p style="font-size: 18px;">See the images below for the end results once the protocol has been followed.</p>
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                  <div style="border-style: solid; border-color: rgb(11,33,10); border-radius: 25px;">
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                    <img width="100%" style="border-style: solid; border-color: rgb(11,33,10); border-radius: 25px;" src="//2017.igem.org/wiki/images/c/c0/IGEM-York-PDMS-and-PDMSChamber.jpg">
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                <li><em>Moulded PDMS and PDMS constructed chamber.</em></li>
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                    <img width="100%" style="border-style: solid; border-color: rgb(11,33,10); border-radius: 25px;" src="//2017.igem.org/wiki/images/1/18/IGEM-York-Polyacryl-Piece-Real.jpg">
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                  </div>
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                </li>
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                <li><em>Poly-acryl piece.</em></li>
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                <li>
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                  <div style="border-style: solid; border-color: rgb(11,33,10); border-radius: 25px;">
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                    <img width="100%" style="border-style: solid; border-color: rgb(11,33,10); border-radius: 25px;" src="//2017.igem.org/wiki/images/3/3d/IGEM-York-Polyacryl-Chamber-Real.jpg">
 +
                  </div>
 +
                </li>
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                <li><em>Poly-acryl constructed chamber.</em></li>
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              </ul>
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            <center>
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          </div>
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        </div>
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      </center>
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      <p style="font-size: 18px;">Please keep in mind when using this chamber design (or similar) that, due to it's low volume capacity, a slow pumping rate is required to prevent motion blur during observations. We used a 3V peristaltic pump with a flow rate on order millilitres, though this was still considerably faster than our camera was able to capture. Fortunately, with small peristaltic pumps, the flow is not constant; there are periods wherein the fluid stops moving completely. This allows for non-blurred images to be captured.</p>
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Latest revision as of 16:29, 31 October 2017

YORK


Hardware

Upright DIHM & Analysis Chamber


Upright DIHM

As outlined on the Description page, we made our microscope out of an aluminium diecast box, a piece of profile extrusion and some plastic blocks. The designs are available via our Downloads page. Once all the parts are acquired, the following assembly process should be used. We have provided step by step instructions, below.


Assembly

Connect the Base and Profile Extrusion


Tap the holes in the profile extrusion so that it can be screwed onto the base as shown.



Prepare the Raspberry Pi




Connect the Explorer hat PRO and Camera Module V2 to the Raspberry Pi 3 as in the images. Note that we removed the lens from the camera.



Connect the Raspberry Pi


Screw the Camera into the position shown using nylon (non-conductive) screws. Connect the power cable to the Pi through the back of the base. This is also where HDMI/USB connections should be made.



Build the Circuitry


We used a 635 nm laser diode and corresponding socket from Thorlabs. Soldering the socket prevents heat damage to the diode itself. Our variable resistor (potentiometer) had a maximum value of 200 Ω.



Connect the Laser


Feed the wires from the circuitry through the profile extrusion, as shown, then connect the positive to the Explorer Hat's 5V output and negative to ground. At this point, the Pi can be sealed inside the diecast box, by adding the base plate.



Add the Platforms



Attach the screws and fixings to the platform. (We used Item profile extrusion, so we used their T-slot nut fixings.) Then, slide each of the platforms into place.


Finally, add the top cover to conceal the circuitry.



Congratulations!

Well done! You now have an assembled Digital Inline Holographic Microscope!


Milli-fluidic Analysis Chamber

We have written a protocol detailing the assembly of both iterations of our milli-fluidic chamber. One uses PDMS and the other uses poly-acryl to form the chamber itself while both make use of glass slides.

See the images below for the end results once the protocol has been followed.

  • Moulded PDMS and PDMS constructed chamber.
  • Poly-acryl piece.
  • Poly-acryl constructed chamber.

Please keep in mind when using this chamber design (or similar) that, due to it's low volume capacity, a slow pumping rate is required to prevent motion blur during observations. We used a 3V peristaltic pump with a flow rate on order millilitres, though this was still considerably faster than our camera was able to capture. Fortunately, with small peristaltic pumps, the flow is not constant; there are periods wherein the fluid stops moving completely. This allows for non-blurred images to be captured.


  • ABOUT US
  • We are an overgraduate team representing the University of York.
  • Our Quicker Way to Analyse Co-Cultures (QWACC) is our entry into the Hardware track for iGEM 2017.
    •