Difference between revisions of "Team:Cambridge-JIC/Make Your Own"

 
(81 intermediate revisions by 5 users not shown)
Line 2: Line 2:
 
<html>
 
<html>
  
−
<section style="background-color:#fff">
+
<style>
−
    <div class="slide" style="min-height:0px">
+
img
−
        <div style="width: 80%; margin: 30px 50px;color:#000">
+
{
−
<h1 style="line-height:1.295em"> Make Your Own </h1>
+
filter: grayscale(1);
−
</div></div></section>
+
-webkit-filter: grayscale(1);
 +
-moz-filter: grayscale(1);
 +
-o-filter: grayscale(1);
 +
-ms-filter: grayscale(1);
 +
}
  
−
<style>
+
img:hover
−
            #cam-quiz {
+
{
−
                background-color: #fff;
+
filter: grayscale(0);
−
                border: 0px;
+
-webkit-filter: grayscale(0);
−
            }
+
-moz-filter: grayscale(0);
 +
-o-filter: grayscale(0);
 +
-ms-filter: grayscale(0);
 +
}
  
−
            .cam-quiz-question, .cam-quiz-result {
+
.slide {
−
                border: 5px solid;
+
padding: 50px;
−
                border-color: #a3c1ad;
+
}
−
                padding: 5px;
+
−
                margin: 0px;
+
−
            }
+
  
−
            .cam-quiz-question {
+
</style>
−
                background-color: #fff;
+
−
            }
+
  
−
            .cam-quiz-answer {
+
<section style="background-color:#fff">
−
                border: 1px solid green;
+
    <div class="slide" style="min-height:0px">
−
                background-color: white;
+
        <div style="width: 100%; margin: 10px 0px;color:#000">
−
                color: black;
+
<center><h1 style="line-height:1.295em"> Make Your Own OpenScope</h1></center>
−
                display: inline-block;
+
<hr>
−
                padding: 0 1em;
+
<center><p>If you want to make your very own OpenScope, this is the page for you!</p></center>
−
                cursor: pointer;
+
<hr>
−
                margin: 0 0.2em;
+
</div></div></section>
−
            }
+
  
−
          .cam-quiz-answer:hover, .cam-quiz-selected {
+
<section style="background-color:#3d3d3d">
−
                background-color: green;
+
    <div class="slide">
−
                color: white;
+
        <div style="width: 100%; padding: 0%; margin: 10px 0px;color:#fff">
−
            }
+
<center><p>We are dedicated to making the OpenScope easy to assemble and use, even for the inexperienced user. We have put together a detailed instruction and compressed all 3d-printable designs into a single archive. Get started with OpenScope.</p></center>
 +
<center><img src="https://static.igem.org/mediawiki/2015/8/81/CamJIC-gallery12.jpeg" style="width:500px;margin:10px"></center>
 +
<center><a class="btn btn-default" href="//2015.igem.org/wiki/images/5/57/CamJIC-MYO.pdf" role="button" style="color:#444;border-color:#fff;margin:10px">instructions</a><a class="btn btn-default" href="//2015.igem.org/wiki/images/d/d5/CamJIC-OpenScope.zip" role="button" style="color:#444;border-color:#fff;margin:10px">printables</a><a class="btn btn-default" href="//2015.igem.org/wiki/images/d/d0/CamJIC-OpenScope-BOM.pdf" role="button" style="color:#444;border-color:#444;margin:10px">bill of materials</a></center>
  
−
            .cam-quiz-answer.cam-quiz-selected {
+
</div></div></section>
−
                font-weight: bold;
+
−
            }
+
  
−
            .cam-quiz-result {
+
<section style="background-color:#fff">
−
                background-color: #fff;
+
    <div class="slide" style="min-height:0px">
−
            }
+
         <div style="width: 100%; padding: 0%; margin: 10px 0px;color:#000">
−
        </style>
+
<center><p>For software installation instructions, and tips on using the Raspberry Pi, visit the <a href="//2015.igem.org/Team:Cambridge-JIC/Downloads#Software" class="blue">Software Downloads</a> section.</p></center>
−
         <script>
+
</div></div></section>
−
            quiz = function(elem){
+
−
                this.elem = $(elem);
+
−
                this.steps = [];
+
  
−
                this.step = function(question, answers) {
+
<section style="background-color:#3d3d3d">
−
                    this.question = question;
+
    <div class="slide"><center>
−
                    this.answers = {};
+
        <div style="width: 100%; padding: 0%; margin: 10px 0px;color:#fff">
−
                    this.bind = function(target, keys) {
+
<center><h3>Video Tutorials</h3></center>
−
                        if (typeof keys === "undefined") {
+
</div>
−
                            keys = Object.keys(this.answers);
+
        <video style="width:80%; margin:20px" controls poster="//2015.igem.org/wiki/images/f/f2/CamJIC-Home_Home.png">
−
                        }
+
            <source src="//2015.igem.org/wiki/images/f/fa/CamJIC-Video-Setup.mp4" type="video/mp4">
 +
        </video>
 +
        <p>Assemble the OpenScope chassis<hr>Having problems seeing the video above? Download the video <a href="//2015.igem.org/wiki/images/f/fa/CamJIC-Video-Setup.mp4" class="blue">here</a>.</p>
 +
<hr>
  
−
                        for (var i=0; i<keys.length; i++) {
+
<video style="width:80%; margin:20px" controls poster="//2015.igem.org/wiki/images/f/f2/CamJIC-Home_Home.png">
−
                            key = keys[i];
+
            <source src="//2015.igem.org/wiki/images/7/78/CamJIC-Video-Epicube.mp4" type="video/mp4">
−
                            this.answers[key].target = target;
+
        </video>
−
                        }
+
        <p>Assemble the OpenScope optics<hr>Having problems seeing the video above? Download the video <a href="//2015.igem.org/wiki/images/7/78/CamJIC-Video-Epicube.mp4" class="blue">here</a>.</p>
−
                    };
+
<hr>
−
                    this.elem = function(quiz, index) {
+
−
                        elem = $('<div class="cam-quiz-question">');
+
−
                        elem.append($('<h3>').text(this.question));
+
−
                        for (key in this.answers) {
+
−
                            elem.append($('<div class="cam-quiz-answer">')
+
−
                                .text(this.answers[key].answer)
+
−
                                .data("key", key)
+
−
                                .data("step", this)
+
−
                                .data("quiz", quiz)
+
−
                                .data("index", index)
+
−
                                .click(function(){
+
−
                                    key = $(this).data("key");
+
−
                                    step = $(this).data("step");
+
−
                                    quiz = $(this).data("quiz");
+
−
                                    index = $(this).data("index");
+
−
                                    ref = quiz.steps[index];
+
−
                                    ref.elem.find('.cam-quiz-selected').removeClass('cam-quiz-selected');
+
−
                                    $(this).addClass('cam-quiz-selected');
+
  
−
                                    for (var i=quiz.steps.length; --i>index;) {
+
<video style="width:80%; margin:20px" controls poster="//2015.igem.org/wiki/images/f/f2/CamJIC-Home_Home.png">
−
                                        quiz.steps[i].elem.remove();
+
            <source src="//2015.igem.org/wiki/images/0/06/CamJIC-Video-Demonstration.mp4" type="video/mp4">
−
                                        quiz.steps.pop();
+
        </video>
−
                                    }
+
        <p>Using the OpenScope<hr>Having problems seeing the video above? Download the video <a href="//2015.igem.org/wiki/images/0/06/CamJIC-Video-Demonstration.mp4" class="blue">here</a>.</p>
 +
<hr>
 +
  </center> </div>
 +
</section>
  
−
                                    quiz.steps[index].option = key;
 
−
                                    nstep = step.answers[key].target;
 
−
                                    switch (typeof nstep) {
 
−
                                        case "object":
 
−
                                            var nindex = quiz.steps.length;
 
−
                                            var nref = {
 
−
                                                'step': nstep,
 
−
                                                'elem': nstep.elem(quiz, nindex),
 
−
                                                'option': undefined
 
−
                                            };
 
−
                                            quiz.steps.push(nref);
 
−
                                            quiz.elem.append(nref.elem);
 
−
                                            break;
 
−
                                        case "function":
 
−
                                            options = [];
 
−
                                            for (var i=0; i<quiz.steps.length; i++) {
 
−
                                                options.push(quiz.steps[i].option);
 
−
                                            }
 
−
                                            var nref = {
 
−
                                                'step': undefined,
 
−
                                                'elem': $('<div class="cam-quiz-result">')
 
−
                                                    .append(nstep(options)),
 
−
                                                'option': undefined
 
−
                                            };
 
−
                                            quiz.steps.push(nref);
 
−
                                            quiz.elem.append(nref.elem);
 
−
                                            break;
 
−
                                        default:
 
−
                                            alert("Quiz error! Please contact the site maintainers....");
 
−
                                            break;
 
−
                                    }
 
−
                                }));
 
−
                        }
 
−
                        return elem;
 
−
                    };
 
  
−
                    for (key in answers) {
+
<section style="background-color:#fff">
−
                        answer = answers[key];
+
    <div class="slide" style="min-height:0px">
−
                        this.answers[key] = {
+
        <div style="width: 100%; margin: 10px 0px;color:#000">
−
                            'answer': answer,
+
<h3>FAQs</h3>
−
                            'target': undefined
+
<p><b>What’s the difference between manual and motorised modes?</b><br>
−
                        };
+
The microscope has 3 knobs: two of them are used to pan across the sample, and one is used to focus. In manual mode, these knobs are controlled by hand. In motorised mode, they are instead connected to stepper motors. This enables you to program your own panning/focusing routines, and to operate the OpenScope remotely: e.g. when it is in an incubator, or in a different lab.</p>
−
                    }
+
<p><b>What is the difference between bright-field, dark-field and fluorescence modes?</b><br>
−
                };
+
Bright-field is the simplest of all imaging modes: just the sample, backlit by a white light source (LED). Bright-field microscopy does not give very good contrast, so it works best for stained samples, or intrinsically colourful samples.
 +
<br>For unstained samples, dark-field microscopy gives better contrast. The dark-field set-up is very similar to that of bight-field, but with the addition of a dark disc (what we call the dark-field tube) in between the white light and the sample. This stops direct illumination from reaching the objective, and so the only recorded light is that scattered by the sample. The main issue with dark-field is that it gives images with very low light levels.<br>
 +
And, finally, fluorescence microscopy allows the imaging of fluorescent proteins (FPs). When excited by light of a specific wavelength (the excitation wavelength), these proteins emit light at a different wavelength (the emission wavelength). Each FP has its own excitation and emission wavelengths. This is why, for each specific FP you will need different LEDs for illumination and different filter sets. For a more detailed explanation on how fluorescence works, and how to pick the filters, refer to our <a href="//2015.igem.org/Team:Cambridge-JIC/Modeling" class="blue">Modeling</a> page.</p>
 +
<p><b>How do I set up my 3D printer?</b><br>
 +
You will need to print your parts using PLA filament. Check out our <a href="//2015.igem.org/Team:Cambridge-JIC/3D_Printing" class="blue">3D printing guide</a>.</p>
 +
<p><b>What if I don’t have a 3D printer?</b><br>
 +
You can send the files from the archive to a local 3D-printing service and they will ship you the printed parts.</p>
 +
<p><b>What are STL and SCAD files?</b><br>
 +
If you want to view a 3D object, you will need the STL file. Use your 3D printer's own software, or download OpenSCAD. If you want to edit one of these objects, open the SCAD file and edit it using OpenSCAD. For printing, the STL file is sufficient.</p>
  
−
                this.start = function(step) {
+
</div></div></section>
−
                    index = this.steps.length;
+
−
                    ref = {
+
−
                        'step': step,
+
−
                        'elem': step.elem(this, index),
+
−
                        'option': undefined
+
−
                    };
+
−
                    this.steps.push(ref);
+
−
                    this.elem.append(ref.elem);
+
−
                };
+
−
            };
+
−
 
+
−
            $(document).ready(function(){
+
−
                q = new quiz('#cam-quiz');
+
−
 
+
−
                step0 = new q.step("Tell us which options you'd like for your microscope.", {
+
−
                    1: "Okay!"
+
−
                });
+
−
                step1 = new q.step("Besides bright-field, do you want dark-field imaging?", {
+
−
                    0: "Yes",
+
−
                    1: "No"
+
−
                });
+
−
                step2a = new q.step("Do you need to image GFP fluorescence?", {
+
−
                    0: "Yes",
+
−
                    1: "No"
+
−
                });
+
−
                step2b = new q.step("Do you need to image RFP fluorescence?", {
+
−
                    0: "Yes",
+
−
                    1: "No"
+
−
                });
+
−
                step2c = new q.step("Do you need to image other fluorescent proteins, e.g. YFP?", {
+
−
                    0: "Yes",
+
−
                    1: "No"
+
−
                });
+
−
                step3 = new q.step("Do you want your microscope to be manual, motorised, or will you need to swap between both?", {
+
−
                    0: "Manual only",
+
−
                    1: "Motorised only",
+
−
                    2: "Both",
+
−
                });
+
−
                step4 = new q.step("Do you want the microscope to be fully battery-powered? This is ideal for field-work.", {
+
−
                    0: "Yes",
+
−
                    1: "No"
+
−
                });
+
−
 
+
−
final = function(options) {
+
−
      window.location.href="#CC0";
+
−
      ret = '<h3>Thanks!</h3><br/><table><tr><th>Item</th><th>Number</th></tr>'
+
−
      if(options[1] == 0) {
+
−
          ret += '<tr><td>jsjdjd</td><td>1</td></tr>'
+
−
      } else {
+
−
          ret += '<tr><td>jsjdjd</td><td>2</td></tr>'
+
−
      }
+
−
      ret += '</table>'
+
−
      return $('<div>').html(ret)
+
−
}
+
−
 
+
−
                step0.bind(step1, [1]);
+
−
 
+
−
                step1.bind(step2a, [0]);
+
−
                step1.bind(step2a, [1]);
+
−
 
+
−
                step2a.bind(step2b, [0]);
+
−
                step2a.bind(step2b, [1]);
+
−
 
+
−
                step2b.bind(step2c, [0]);
+
−
                step2b.bind(step2c, [1]);
+
−
 
+
−
                step2c.bind(step3, [0]);
+
−
                step2c.bind(step3, [1]);
+
−
 
+
−
                step3.bind(step4, [0]);
+
−
                step3.bind(step4, [1]);
+
−
                step3.bind(step4, [2]);
+
−
 
+
−
                step4.bind(final, [0]);
+
−
                step4.bind(final, [1]);
+
−
+
−
                q.start(step0);
+
−
            });
+
  
−
         </script>
+
<!--
 +
<style>img.diagram { width: 80%; margin: 30px auto; display: block; }</style>
 +
<link href="//2015.igem.org/Team:Cambridge-JIC/Assets/Quiz_css?action=raw&ctype=text/css" rel="stylesheet">
 +
<script src="//2015.igem.org/Team:Cambridge-JIC/Assets/Quiz_js?action=raw&ctype=text/javascript"></script>
 +
         <script src="//2015.igem.org/Team:Cambridge-JIC/Make_Your_Own_js?action=raw&ctype=text/javascript"></script>
  
−
    <section style="background:white">
+
<section style="background:white">
 
<div class="slide">
 
<div class="slide">
−
<div style="width: 80%; margin: -40px 50px;color:black;min-height:0px">
+
<div style="width: 80%; margin:10px;color:black;min-height:0px">
−
         <div id="cam-quiz" style="width: 80%; margin: 10px 50px">
+
         <div id="cam-quiz" style="width: 80%; margin: 10px 50px; padding-bottom: 50px;">
  
−
If you want to make your very own OpenScope, this is the page for you!<br/>
 
 
<br/>
 
<br/>
−
OpenScope is a modular microscope: you can use it in manual mode, or you can add motors for finer control. It is very easy to swap between manual and motorized modes.<br/>
 
 
<br/>
 
<br/>
−
You can also use bright-field imaging only, or extend the microscope to include fluorescence imaging or dark-field imaging.<br/>
+
OpenScope is a modular microscope: you can use it in manual mode, or you can add motors for finer control. It is very easy to swap between manual and motorized modes. It is also possible to make the microscope fully battery-powered: ideal for fieldwork.<br/>
−
<br/>
+
−
It is also possible to make the microscope fully battery-powered (ideal for fieldwork!).
+
 
<br/>
 
<br/>
 +
You can use your OpenScope for bright-field imaging only, or extend it to include dark-field and even fluorescence (we have succeeded in imaging GFP only). Check out our <a href="//2015.igem.org/Team:Cambridge-JIC/Modeling" class="blue">Modeling</a> pade to find out how to pick the filters you need for imaging any fluorescent molecule. And if you manage to get it working, we'd love to hear about it!<br/>
 
<br/>
 
<br/>
 
</div>
 
</div>
 
<noscript>Enable JavaScript to be able to display the quiz properly.</noscript></div>
 
<noscript>Enable JavaScript to be able to display the quiz properly.</noscript></div>
 +
 
     </section>
 
     </section>
−
 
+
-->
−
 
+
<section class="slide" style="color: black; min-height:0">
−
 
+
<a rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/"><img alt="Creative Commons Licence" style="border-width:0" src="https://i.creativecommons.org/l/by-sa/4.0/88x31.png" /></a><br /><span xmlns:dct="http://purl.org/dc/terms/" property="dct:title">Open Scope Documentation</span> by <a xmlns:cc="http://creativecommons.org/ns#" href="//2015.igem.org/Team:Cambridge-JIC" property="cc:attributionName" rel="cc:attributionURL" style="color:#1b4f18;">Simon Swan, Katerina Naydenova, </a> <a href="//www.phy.cam.ac.uk/people/rwb27" style="color:#1b4f18;">Richard Bowman</a> is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/" style="color:#1b4f18;">Creative Commons Attribution-ShareAlike 4.0 International License</a>. Please note that all contributions to 2015.igem.org are considered to be released under the Creative Commons Attribution.
 +
</section>
 
</html>
 
</html>
 
{{:Team:Cambridge-JIC/Templates/Footer}}
 
{{:Team:Cambridge-JIC/Templates/Footer}}

Latest revision as of 03:41, 19 September 2015

CAMBRIDGE-JIC

Make Your Own OpenScope

If you want to make your very own OpenScope, this is the page for you!

We are dedicated to making the OpenScope easy to assemble and use, even for the inexperienced user. We have put together a detailed instruction and compressed all 3d-printable designs into a single archive. Get started with OpenScope.

instructionsprintablesbill of materials

For software installation instructions, and tips on using the Raspberry Pi, visit the Software Downloads section.

Video Tutorials

Assemble the OpenScope chassis

Having problems seeing the video above? Download the video here.

Assemble the OpenScope optics

Having problems seeing the video above? Download the video here.

Using the OpenScope

Having problems seeing the video above? Download the video here.

FAQs

What’s the difference between manual and motorised modes?
The microscope has 3 knobs: two of them are used to pan across the sample, and one is used to focus. In manual mode, these knobs are controlled by hand. In motorised mode, they are instead connected to stepper motors. This enables you to program your own panning/focusing routines, and to operate the OpenScope remotely: e.g. when it is in an incubator, or in a different lab.

What is the difference between bright-field, dark-field and fluorescence modes?
Bright-field is the simplest of all imaging modes: just the sample, backlit by a white light source (LED). Bright-field microscopy does not give very good contrast, so it works best for stained samples, or intrinsically colourful samples.
For unstained samples, dark-field microscopy gives better contrast. The dark-field set-up is very similar to that of bight-field, but with the addition of a dark disc (what we call the dark-field tube) in between the white light and the sample. This stops direct illumination from reaching the objective, and so the only recorded light is that scattered by the sample. The main issue with dark-field is that it gives images with very low light levels.
And, finally, fluorescence microscopy allows the imaging of fluorescent proteins (FPs). When excited by light of a specific wavelength (the excitation wavelength), these proteins emit light at a different wavelength (the emission wavelength). Each FP has its own excitation and emission wavelengths. This is why, for each specific FP you will need different LEDs for illumination and different filter sets. For a more detailed explanation on how fluorescence works, and how to pick the filters, refer to our Modeling page.

How do I set up my 3D printer?
You will need to print your parts using PLA filament. Check out our 3D printing guide.

What if I don’t have a 3D printer?
You can send the files from the archive to a local 3D-printing service and they will ship you the printed parts.

What are STL and SCAD files?
If you want to view a 3D object, you will need the STL file. Use your 3D printer's own software, or download OpenSCAD. If you want to edit one of these objects, open the SCAD file and edit it using OpenSCAD. For printing, the STL file is sufficient.

Creative Commons Licence
Open Scope Documentation by Simon Swan, Katerina Naydenova, Richard Bowman is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License. Please note that all contributions to 2015.igem.org are considered to be released under the Creative Commons Attribution.