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

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<h2> Project Description </h2>
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<p>Tell us about your project, describe what moves you and why this is something important for your team.</p>
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<h5>What should this page contain?</h5>
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<li> A clear and concise description of your project.</li>
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<li>A detailed explanation of why your team chose to work on this particular project.</li>
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<li>References and sources to document your research.</li>
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<h4>Advice on writing your Project Description</h4>
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We encourage you to put up a lot of information and content on your wiki, but we also encourage you to include summaries as much as possible. If you think of the sections in your project description as the sections in a publication, you should try to be consist, accurate and unambiguous in your achievements.
 
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Judges like to read your wiki and know exactly what you have achieved. This is how you should think about these sections; from the point of view of the judge evaluating you at the end of the year.
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        <div style="width: 100%; padding: 0% 10%; margin: 30px 0px;color:#000;position:absolute;top:50%">
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            <center><p><span class="dark" style="font-size:340%">Microscopy awaits you...</span></p></center>
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        <center><p><span class="dark" style="font-size:170%">Cambridge-JIC brings you OpenScope: the foundation to a new era of accessible microscopy.</span></p></center>
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<h4>References</h4>
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<p>iGEM teams are encouraged to record references you use during the course of your research. They should be posted somewhere on your wiki so that judges and other visitors can see how you though about your project and what works inspired you.</p>
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<p><span class="dark" style="font-size:170%">The chassis</span> is 3D printed, allowing simple modification. The plastic is cheap, biodegradable and flexible. Stage translation, based on work by Dr Richard Bowman [1], makes use of the flexibility to give fine control.</p>
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<p><span class="dark" style="font-size:170%">The mechanics</span> of the stage can be automated using stepper motors. The user has remote control of the microscope, and can introduce tailor-made programs to facilitate their experiments.</p>
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<hr>
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<p><span class="dark" style="font-size:170%">The optics</span> are low-cost, low-energy and modular. Illumination using LEDs means reducing power consumption and cost. A Raspberry Pi camera makes the microscope digital, and an epi-fluorescence cube makes imaging GFP a reality. With sub-micrometer resolution in brightfield and darkfield modes, you are ready to image single cells or whole tissues.</p>
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<p><span class="dark" style="font-size:170%">The software</span> uses OpenCV and forms a core part of the project. The Webshell gives you real-time control over the microscope live-stream: from time-lapse to scale-bars. MicroMaps uses image stitching and sample recognition algorithms to give you the whole sample field in one, ready for annotation and screening. Autofocus capabilities allow automation of OpenScope’s motors, letting you image dynamic samples without supervision.</p>
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<p><span class="dark" style="font-size:170%">The documentation</span> is comprehensive, non-proprietary and easy to access. And its licensed to make sure it stays that way.</p>
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<p><span class="dark" style="font-size:170%">The community</span> of ‘makers’ is free to develop, modify and redistribute the documentation. OpenScope can evolve, improve and adapt to different needs.</p>
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<hr>
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<p><span class="dark" style="font-size:170%">The overall cost</span> is below £200, orders of magnitude below commercial lab microscopes.</p>
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<p style="font-size:80%">[1] Sharkey, J., Foo, D., Kabla, A., Baumberg, J. and Bowman, R. (2015). <i>A one-piece 3D printed microscope and flexure translation stage.</i><a href="http://arxiv.org/abs/1509.05394" class="blue">[online]</a>  Arxiv.org. [Accessed 18 Sep. 2015].</p>
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<h4>Inspiration</h4>
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<p>See how other teams have described and presented their projects: </p>
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<p><span class="dark" style="font-size:170%">The result?</span></p>
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<p>A microscopy solution for synthetic biologists, letting <span class="dark" style="font-size:170%">researchers</span> tailor the microscope to their needs. Image in the incubator, fume-hood or the field using remote access and battery power, or use OpenScope for rapid preliminary screening.</p>
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<p>A microscopy solution for <span class="dark" style="font-size:170%">schools</span>, providing education in programming, optics and one of the most ubiquitous techniques in biological research: fluorescence imaging.</p>
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<hr>
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<p>A microscopy solution for laboratories with small budgets, based on low-cost and easily sourced components. The potential of Openscope to increase access to microscopy in <span class="dark" style="font-size:170%">developing countries</span> has been a key part of the design process from day one. </p>
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<li><a href="https://2014.igem.org/Team:Imperial/Project"> Imperial</a></li>
 
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<li><a href="https://2014.igem.org/Team:UC_Davis/Project_Overview"> UC Davis</a></li>
 
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<li><a href="https://2014.igem.org/Team:SYSU-Software/Overview">SYSU Software</a></li>
 
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Latest revision as of 21:17, 18 September 2015

CAMBRIDGE-JIC

Microscopy awaits you...

Cambridge-JIC brings you OpenScope: the foundation to a new era of accessible microscopy.

The chassis is 3D printed, allowing simple modification. The plastic is cheap, biodegradable and flexible. Stage translation, based on work by Dr Richard Bowman [1], makes use of the flexibility to give fine control.

The mechanics of the stage can be automated using stepper motors. The user has remote control of the microscope, and can introduce tailor-made programs to facilitate their experiments.

The optics are low-cost, low-energy and modular. Illumination using LEDs means reducing power consumption and cost. A Raspberry Pi camera makes the microscope digital, and an epi-fluorescence cube makes imaging GFP a reality. With sub-micrometer resolution in brightfield and darkfield modes, you are ready to image single cells or whole tissues.

The software uses OpenCV and forms a core part of the project. The Webshell gives you real-time control over the microscope live-stream: from time-lapse to scale-bars. MicroMaps uses image stitching and sample recognition algorithms to give you the whole sample field in one, ready for annotation and screening. Autofocus capabilities allow automation of OpenScope’s motors, letting you image dynamic samples without supervision.

The documentation is comprehensive, non-proprietary and easy to access. And its licensed to make sure it stays that way.

The community of ‘makers’ is free to develop, modify and redistribute the documentation. OpenScope can evolve, improve and adapt to different needs.

The overall cost is below £200, orders of magnitude below commercial lab microscopes.

[1] Sharkey, J., Foo, D., Kabla, A., Baumberg, J. and Bowman, R. (2015). A one-piece 3D printed microscope and flexure translation stage.[online] Arxiv.org. [Accessed 18 Sep. 2015].

The result?

A microscopy solution for synthetic biologists, letting researchers tailor the microscope to their needs. Image in the incubator, fume-hood or the field using remote access and battery power, or use OpenScope for rapid preliminary screening.

A microscopy solution for schools, providing education in programming, optics and one of the most ubiquitous techniques in biological research: fluorescence imaging.

A microscopy solution for laboratories with small budgets, based on low-cost and easily sourced components. The potential of Openscope to increase access to microscopy in developing countries has been a key part of the design process from day one.