Difference between revisions of "Team:Cambridge-JIC/Downloads"

 
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<section style="background-color: #fff">
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     <div class="slide" style="min-height:0px">
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         <div class="team">
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         <div style="width: 100%; padding: 0% 10%; margin: 30px 0px;color:#000;min-height:0px">
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            <h2>Downloads</h2>
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<center><h1>Downloads</h1></center>
 +
<center><p style="color:#444">Every single file you can get from our Wiki. All in one place.</p></center>
 +
    </div>
 +
</section>
  
 +
<section style="background-color: #444" id="OpenScope">
 +
    <div class="slide">
 +
        <div style="width: 100%; padding: 0% 10%; margin: 30px 0px;color:#fff;min-height:0px">
 +
            <h3>OpenScope</h3>
 +
<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. For more help and troubleshooting - visit our <a href="//2015.igem.org/Team:Cambridge-JIC/Make_Your_Own" class="blue">Make Your Own</a> page. There you can also find some helpful (and entertaining) videos. With these resources available, everyone will be able to build and use the OpenScope. In fact, we think putting together the OpenScope is a great engineering experience for beginners.</p>
 +
<center><img src="//2015.igem.org/wiki/images/0/0e/CamJIC-OpenScope-Shadow.png" width="200px;float:left"></center><br>
 +
<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></center>
 +
</div></div></section>
  
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            <section style="background-color:#676566;width:100%">
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<section style="background-color: #fff" id="Learn">
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             <h3>Optics Housing: Raspberry Pi camera mounting modules</h3>
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    <div class="slide">
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            <div class="face" style="background-image: url(//2015.igem.org/wiki/images/1/1c/CamJIC-Downloads-CameraMount.png)">
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        <div style="width: 100%; padding: 0% 10%; margin: 30px 0px;color:#000;min-height:0px">
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                <div class="blur"></div>
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             <h3>Learning Resources</h3>
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                <div class="profile">
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<p><b>Licensing Guide</b></p>
−
                    <h3>Camera Mount</h3>
+
<p>As part of our Human Practices, "Open-Source Hardware: An iGEM Guide" is available as a starting point for future teams on the Hardware Track:</p>
−
                    <p>Module for housing the Raspberry Pi Camera board and the detached inverted lens on top. The distance is optimised for focusing the image onto the sensor. This module is compatible with the camera holders.</p>
+
<center><a class="btn btn-default" href="//2015.igem.org/wiki/images/d/db/CamJIC-Practices-Guide.pdf" role="button" style="color:#444;border-color:#bbb">download guide</a></center>
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                </div>
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<!--<p><b>Optics Bench</b></p>
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            </div>
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<p>What path will light take through the microscope? Which lenses do we need, and how do we arrange them? These are some of the very first questions one must answer when designing a microscope. Optical design professionals construct and optimize their light paths using commercial software, then construct their physical prototypes using an optical table. These tables can cost over 10 000 GBP as they are designed to maximise the stability of the optical elements, by isolating them from any vibrations that may be transmitted through the legs. For our OpenScope, this is rather excessive. So here is our low-cost, open-source alternative! 3D print these parts, get a magnetic board, some cylindrical magnets, and experiment.</p>-->
 +
<p><b>Microscopy Workshop</b></p>
 +
<p>As part of our Outreach, we organised a microscopy workshop. The teaching resources used are available here:</p>
 +
<center><a class="btn btn-default" href="//2015.igem.org/wiki/images/4/40/CamJIC-Outreach-Microscopy.pdf" role="button" style="color:#444;border-color:#bbb;;margin:10px">Microscopy Workshop</a></center>
 +
<p><b>Programming the Arduino Guide</b></p>
 +
<p>Want to learn to program Arduinos? As part of our outreach workshop, we introduced school students to the basics. The resources we made can be useful to anyone:</p>
 +
<center><a class="btn btn-default" href="//2015.igem.org/wiki/images/a/a7/CamJIC-Outreach-ArduinoBooklet.pdf" role="button" style="color:#444;border-color:#bbb;;margin:10px">Arduino Booklet</a>
 +
<a class="btn btn-default" href="//2015.igem.org/wiki/images/a/a1/CamJIC-Outreach-ArduinoNotes.pdf" role="button" style="color:#444;border-color:#bbb;;margin:10px">Arduino Notes</a>
 +
<a class="btn btn-default" href="//2015.igem.org/wiki/images/0/06/CamJIC-Outreach-ArduinoEx.pdf" role="button" style="color:#444;border-color:#bbb;;margin:10px">Arduino Exercises</a>
 +
<a class="btn btn-default" href="//2015.igem.org/wiki/images/0/04/CamJIC-Outreach-ArduinoEx3.txt" role="button" style="color:#444;border-color:#bbb;;margin:10px">Exercise 3 Solution</a>
 +
<a class="btn btn-default" href="//2015.igem.org/wiki/images/d/d1/CamJIC-Outreach-ArduinoEx4.txt" role="button" style="color:#444;border-color:#bbb;;margin:10px">Exercise 4 Code</a>
 +
<a class="btn btn-default" href="//2015.igem.org/wiki/images/d/d9/CamJIC-Outreach-ArduinoEx4S.txt" role="button" style="color:#444;border-color:#bbb;;margin:10px">Exercise 4 Solution</a></center>
 +
<p><b>Filter Choice Modeling</b></p>
 +
<p>Thinking of imaging a fluorescent protein? Download our Python script that helps you choose the most appropriate filters and mirrors for your microscope. For more info, visit the <a href="https://2015.igem.org/Team:Cambridge-JIC/Modeling" class="blue">Modeling</a> page.</p>
 +
<center><a class="btn btn-default" href="//2015.igem.org/wiki/images/b/b4/CamJIC-Modeling.zip" role="button" style="color:#444;border-color:#bbb">download package</a></center>
 +
</div></div></section>
  
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            <div class="face" style="background-image: url()">
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<section style="background-color: #444" id="Tech">
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                <div class="blur"></div>
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    <div class="slide">
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                <div class="profile">
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        <div style="width: 100%; padding: 0% 10%; margin: 30px 0px;color:#fff;min-height:0px">
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                    <h3>Camera Mount for Fluorescence</h3>
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            <h3>Technical Specifications</h3>
−
                    <p>Camera mount housing the Raspberry Pi Cam board, the inverted lens and the fluorescence cube (two filters, dichroic mirror and an LED) inside. A true masterpiece. For use in fluorescence microscopy. Compatible with the standard camera holders.</p>
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<p><b>Stage Drift Characterisation</b></p>
−
                </div>
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<p>Stage drift can affect time-lapse imaging. We analysed the drift of our microscope to asses its significance.</p>
−
            </div>
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<center><a class="btn btn-default" href="//2015.igem.org/wiki/images/5/52/CamJIC-Specs-Drift.pdf" role="button" style="color:#444;border-color:#444">download pdf</a></center>
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            </section>
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<p><b>Resolution Assessment</b></p>
 +
<p>Detailed information on the calculations required to determine OpenScope's resolution and to design the optics housing can be found here:</p>
 +
</p><center><a class="btn btn-default" href="//2015.igem.org/wiki/images/8/81/CamJIC-Specs-Optics.pdf" role="button" style="color:#444;border-color:#fff">download pdf</a></center>
 +
<p><b>Translation Precision</b></p>
 +
<p>Information on how the resolution of the translation stage was determined is provided here:</p>
 +
<center><a class="btn btn-default" href="//2015.igem.org/wiki/images/4/4d/CamJIC-Specs-Movement.pdf" role="button" style="color:#444;border-color:#fff">download pdf</a></center>
 +
<p><b>Bill of Materials</b></p>
 +
<p>A full Bill of Materials, including cost and source, is available for download here:</p>
 +
<center><a class="btn btn-default" href="https://static.igem.org/mediawiki/2015/d/d0/CamJIC-OpenScope-BOM.pdf" role="button" style="color:#444;border-color:#fff">download pdf</a></center>
 +
<p><b>Power Consumption Analysis</b></p>
 +
<p>Calculating the battery life of our microscope required analysis of its power consumption. The details of this analysis are given below.</p>
 +
<center><a class="btn btn-default" href="//2015.igem.org/wiki/images/7/73/CamJIC-Specs-Power.pdf" role="button" style="color:#444;border-color:#444">download pdf</a></center>
 +
<p><b>Strength and Flexibility Testing</b></p>
 +
<p>Three-point being tests were carried out to characterise the material properties of PLA. Information on the results is available below. In short: OpenScope is stronger than you would expect.</p>
 +
<center><a class="btn btn-default" href="//2015.igem.org/wiki/images/3/37/CamJIC-Specs-Materials.pdf" role="button" style="color:#444;border-color:#fff">download pdf</a></center>
 +
</div></div></section>
  
−
            <section>
 
−
            <h3>Prototyping: optical bench/table</h3>
 
  
−
             <a href="//2015.igem.org/wiki/images/e/e1/CamJIC-CameraAdapterHolderSCAD.zip">
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<section style="background-color: #fff" id="Software">
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            <div class="face" style="background-image: url(//2015.igem.org/wiki/images/4/49/CamJIC-Downloads-CameraHolder.png)">
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    <div class="slide">
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                <div class="blur"></div>
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        <div style="width: 100%; padding: 0% 10%; margin: 30px 0px;color:#000;min-height:0px">
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                <div class="profile">
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             <h3>Software</h3>
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                    <h3>Camera Holder</h3>
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<p><b>Github Repository</b></p>
−
                    <p>A stand for positioning the Raspberry Pi Camera (with its housing) onto the magnetic optical table. Also available in a version compatible with a standard optical rail holder.</p>
+
<p>The full contents of our Github repository are available here:</p>
−
                </div>
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</p><center><a href="http://github.com/sourtin/igem15-sw/" class="btn btn-default btn-lg" style="color:#444;border-color:#444"><i class="fa fa-github"></i>Visit our github</a>&nbsp;&nbsp;<a href="//2015.igem.org/wiki/images/f/fe/CamJIC-Dist-OpenScope-Utilities.zip" class="btn btn-default btn-lg" style="color:#444;border-color:#444;"><i class="fa fa-download"></i>Download All</a></center>
−
            </div>
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<p><b>OpenScope Image</b></p>
−
            </a>
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<p>The NOOBSCOPE SD card image is available here. This gives you everything we've developed for OpenScope. Just a few steps:
 +
<ol>
 +
<li><p>Format your SD card as FAT32 (Windows and Mac users may download the SD Formatter software <a href="//www.sdcard.org/downloads/formatter_4/" class="blue">here</a>; just install, run, and select your SD card in the menu provided).</p></li>
 +
<li><p>Unzip the NOOBSCOPE.zip file and drop all the contents of the NOOBSCOPE directory directly into the SD card.</p></li>
 +
<li><p>Put the SD card into your Raspberry Pi, turn it on, select NOOBSCOPE, and click install!</p></li>
 +
<li><p>Now that you have installed the image, you will notice (if you have plugged in the wifi adapter we recommend) a wifi
 +
network named OPENSCOPE. Connect to this (password is PASSWORD) and point your browser to <a href="https://192.168.0.1:9000/" class="blue">https://192.168.0.1:9000/</a> to start using OpenScope. The default OpenScope login is:<br>
 +
</p><center><code>Username: admin</code></center><br>
 +
<center><code>Password: test<br></code></center>
 +
<p><i>Note: These are different from the username and password on the Pi's OS itself, see below how to change.</i></p></li>
 +
<li><p>To secure the Raspberry Pi:</p>
 +
<ul>
 +
<li><p>Get <a href="http://www.chiark.greenend.org.uk/~sgtatham/putty/" class="blue">PuTTY</a> on Windows and after connecting to the OPENSCOPE network, open PuTTY, set the host to 192.168.0.1 and connect.<br>
 +
</p><center><code>Username: pi</code></center><br>
 +
<center><code>Password: raspberry<br></code></center>
 +
<p><i>Note: You will not see your password when you type it - this is normal and is intended to hide it.</i></p></li>
 +
<li><p>If on Linux/Mac OSX, no need to install anything. Connect to the OPENSCOPE network and open Terminal and run the command:<br></p><center><code>ssh pi@192.168.0.1</code></center><p><br>Enter the password (raspberry) and press enter. You will not be able to see anything as you type your password - this is normal for security.</p></li>
 +
</ul></li>
 +
<li><p>To change the default password, type in:<br>
 +
</p><center><code>passwd</code></center><br><p>
 +
and press enter. You will be prompted about entering your new password.</p></li>
 +
<li><p>To update the OpenScope software to the latest and greatest version, connect an ethernet cable to the Pi and connect it to a router. Then, after opening an ssh connection as above, instead of running passwd, run:<br>
 +
</p><center><code>cd ~/igem15-sw/; git pull</code></center><p><br>
 +
This will pull the latest code and done!</p></li>
 +
</ol>
 +
<p><em>For more detailed instructions, follow those of the official Raspberry Pi foundation <a href="//www.raspberrypi.org/help/noobs-setup/" class="blue">here</a>, substituting Raspbian for NOOBSCOPE where appropriate.</em></p>
 +
<p>Instructions to get started are available in the README file in our Github Repository (see above), or on the <a href="//2015.igem.org/Team:Cambridge-JIC/Make_Your_Own" class="blue">Make Your Own</a> page.</p>
 +
<center><a href="//2015.igem.org/images/Cambridge-JIC-NOOBSCOPE.zip" class="btn btn-default btn-lg" style="color:#444;border-color:#444">NOOBSCOPE</a></center>
 +
<p><b>ImageJ Plug-In</b></p>
 +
<p>OpenScope wouldn't be complete without a plug-in to your favourite microscopy software software. Download it here:</p>
 +
<center><a href="//2015.igem.org/wiki/images/8/8b/CamJIC-Dist-OpenScope-ImageJ.zip" class="btn btn-default btn-lg" style="color:#444;border-color:#444">ImageJ Plugin</a></center>
 +
</div></div></section>
  
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            <div class="face" style="background-image: url(//2015.igem.org/wiki/images/a/af/CamJIC-Downloads-OpticalRailCameraAdapter.png)">
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<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.
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                <div class="blur"></div>
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                <div class="profile">
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                    <h3>Camera Holder</h3>
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                    <p>A stand for positioning the Raspberry Pi Camera (with its housing) into a standard optical rail holder. Also available in a version compatible with a magnetic optical table.</p>
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−
                </div>
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            </div>
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            <a href="//2015.igem.org/wiki/images/d/d4/CamJIC-LEDx15HolderSCAD.zip">
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            <div class="face" style="background-image: url(//2015.igem.org/wiki/images/5/59/CamJIC-Downloads-LEDArray.png)">
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                <div class="profile">
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                    <h3>LED Array</h3>
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                    <p>LED array for brighter illumination of your samples. Compatible with our lens holders.</p>
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                </div>
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            </div>
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            </a>
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            <a href="//2015.igem.org/wiki/images/1/11/LensTube.zip">
 
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                <div class="profile">
 
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                    <h3>Lens Tube</h3>
 
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                    <p>A necessity for alignment of multi-lens optical systems. Customisable and compatible with our lens holders.</p>
 
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                </div>
 
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            </div>
 
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            </a>
 
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            <br />
 
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            <a href="//2015.igem.org/wiki/images/7/79/LensHolderSCAD.zip">
 
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                <div class="profile">
 
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                    <h3>Lens Holder</h3>
 
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                    <p>A stand for positioning your lenses onto the magnetic optical table. Parametrically specified to position the centre of the lens at the same height as other items. Fully customisable for different radii or thicknesses of lenses. Also available in a version compatible with a standard optical rail holder.</p>
 
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                    <h3>Lens Holder</h3>
 
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                    <p>A stand for housing lenses, compatible with standard optical rail holders. Fully customisable for different radii or thicknesses of lenses. Also available in a version for use with the magnetic optical table.</p>
 
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                    <h3>Slide Holder</h3>
 
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                    <p>Slide holder for positioning your microscopy slides vertically on the magnetic optical table. Also available in a version for use with standard optical bench. Currently requires attaching the slide to it with blu-tack. Upgraded version coming soon.</p>
 
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                </div>
 
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                    <p>Slide holder compatible with standard optical rail holders. Also available in a version for use on the magnetic optical table. Currently requires attaching the slide to it with blu-tack. Upgraded version coming soon.</p>
 
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Latest revision as of 03:28, 19 September 2015

CAMBRIDGE-JIC

Downloads

Every single file you can get from our Wiki. All in one place.

OpenScope

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. For more help and troubleshooting - visit our Make Your Own page. There you can also find some helpful (and entertaining) videos. With these resources available, everyone will be able to build and use the OpenScope. In fact, we think putting together the OpenScope is a great engineering experience for beginners.


instructionsprintables

Learning Resources

Licensing Guide

As part of our Human Practices, "Open-Source Hardware: An iGEM Guide" is available as a starting point for future teams on the Hardware Track:

download guide

Microscopy Workshop

As part of our Outreach, we organised a microscopy workshop. The teaching resources used are available here:

Microscopy Workshop

Programming the Arduino Guide

Want to learn to program Arduinos? As part of our outreach workshop, we introduced school students to the basics. The resources we made can be useful to anyone:

Arduino Booklet Arduino Notes Arduino Exercises Exercise 3 Solution Exercise 4 Code Exercise 4 Solution

Filter Choice Modeling

Thinking of imaging a fluorescent protein? Download our Python script that helps you choose the most appropriate filters and mirrors for your microscope. For more info, visit the Modeling page.

download package

Technical Specifications

Stage Drift Characterisation

Stage drift can affect time-lapse imaging. We analysed the drift of our microscope to asses its significance.

download pdf

Resolution Assessment

Detailed information on the calculations required to determine OpenScope's resolution and to design the optics housing can be found here:

download pdf

Translation Precision

Information on how the resolution of the translation stage was determined is provided here:

download pdf

Bill of Materials

A full Bill of Materials, including cost and source, is available for download here:

download pdf

Power Consumption Analysis

Calculating the battery life of our microscope required analysis of its power consumption. The details of this analysis are given below.

download pdf

Strength and Flexibility Testing

Three-point being tests were carried out to characterise the material properties of PLA. Information on the results is available below. In short: OpenScope is stronger than you would expect.

download pdf

Software

Github Repository

The full contents of our Github repository are available here:

Visit our github  Download All

OpenScope Image

The NOOBSCOPE SD card image is available here. This gives you everything we've developed for OpenScope. Just a few steps:

  1. Format your SD card as FAT32 (Windows and Mac users may download the SD Formatter software here; just install, run, and select your SD card in the menu provided).

  2. Unzip the NOOBSCOPE.zip file and drop all the contents of the NOOBSCOPE directory directly into the SD card.

  3. Put the SD card into your Raspberry Pi, turn it on, select NOOBSCOPE, and click install!

  4. Now that you have installed the image, you will notice (if you have plugged in the wifi adapter we recommend) a wifi network named OPENSCOPE. Connect to this (password is PASSWORD) and point your browser to https://192.168.0.1:9000/ to start using OpenScope. The default OpenScope login is:

    Username: admin

    Password: test

    Note: These are different from the username and password on the Pi's OS itself, see below how to change.

  5. To secure the Raspberry Pi:

    • Get PuTTY on Windows and after connecting to the OPENSCOPE network, open PuTTY, set the host to 192.168.0.1 and connect.

      Username: pi

      Password: raspberry

      Note: You will not see your password when you type it - this is normal and is intended to hide it.

    • If on Linux/Mac OSX, no need to install anything. Connect to the OPENSCOPE network and open Terminal and run the command:

      ssh pi@192.168.0.1


      Enter the password (raspberry) and press enter. You will not be able to see anything as you type your password - this is normal for security.

  6. To change the default password, type in:

    passwd

    and press enter. You will be prompted about entering your new password.

  7. To update the OpenScope software to the latest and greatest version, connect an ethernet cable to the Pi and connect it to a router. Then, after opening an ssh connection as above, instead of running passwd, run:

    cd ~/igem15-sw/; git pull


    This will pull the latest code and done!

For more detailed instructions, follow those of the official Raspberry Pi foundation here, substituting Raspbian for NOOBSCOPE where appropriate.

Instructions to get started are available in the README file in our Github Repository (see above), or on the Make Your Own page.

NOOBSCOPE

ImageJ Plug-In

OpenScope wouldn't be complete without a plug-in to your favourite microscopy software software. Download it here:

ImageJ Plugin
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.