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

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             <h1>Microscopy awaits you...</h1>
 
             <h1>Microscopy awaits you...</h1>
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         <h3>Cambridge-JIC iGEM brings you OpenScope: an accessible solution to microscopy.</h3>
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Fluorescence microscopy has become a ubiquitous part of biological research and synthetic biology, but hardware can often be large and prohibitively expensive. This is particularly true for labs with small budgets, including those in the DIY Bio community and developing countries. Queuing systems imposed in labs for use of a few expensive microscopes can make research even more laborious and time-consuming than it needs to be. Furthermore, this makes it almost impossible to perform time-lapse imaging or imaging in environments such as in an incubator or in a fume hood. We aim to provide a well documented, affordable, physically compact, easily modifiable and high quality brightfield/fluorescence microscope to address all of these problems. We are designing it in a modular fashion such that it can be used standalone and also be incorporated into larger frameworks, with various pluggable stages.
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<p><b>The chassis</b> is 3D printed, allowing simple modification. The plastic is cheap, biodegradable and flexible. Stage translation, based on work by Dr Richard Bowman, makes use of the flexibility to give fine control. </p>
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<p><b>The mechanics</b> of the stage can be automated using stepper motors. The user has remote control of the microscope, and can introduce tailor-made programs to [complete] facilitate their experiments.</p>
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<p><b>The optics</b> 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><b>The software</b> 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 and providing autofocus.</p>
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<p><b>The documentation</b> is comprehensive, non-proprietary and easy to access. It is licensed to make sure it stays that way.</p>
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<p><b>The community</b> 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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<p><b>The overall cost</b> is below £100, orders of magnitude below commercial lab microscopes.</p>
 
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<p><b>The result?</b></p>
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The mechanics of our microscope will be 3D printable, and all other parts will be cheap and easy to source. The figure below shows our basic set-up: the sensor and fluorescence cube will move in the Z direction to achieve the necessary focus, whilst the sample will move in the X and Y directions (in order to achieve this translation, we will use Dr Richard Bowman's innovative method, which exploits the flexibility of the 3D printed parts).<br>
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<p>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.</p>
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<p>A microscopy solution for schools, providing education in programing, optics and one of the most ubiquitous techniques in biological research: fluorescence imaging.</p>
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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 developing countries has been a key part of the design process from day one. </p>
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As proof-of-concept, we will develop a fluorescent cube for wild-type GFP and one for RFP. They will be interchangeable as necessary, and can be removed for bright-field imaging. We have achieved 4 micron resolution, both in bright-field and fluorescent modes. We are also developing user-friendly software to control the microscope and automate image processing. We aim to leverage the full computational potential of a digital microscope, carefully considering functional UX design to allow control (locally and also over a network) via a Google Maps-like interface and implementing background image processing, annotation and stitching, as well as allowing fully autonomous operation. As a proof of principle, we are also developing automated screening systems on our microscope architecture.<br>
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We believe that everyone should have access to good education and facilities, regardless of financial status: this is why we want to bring you the best possible low-cost microscope.
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Revision as of 14:26, 16 September 2015

CAMBRIDGE-JIC

Microscopy awaits you...

Cambridge-JIC iGEM brings you OpenScope: an accessible solution to 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, 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 [complete] 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 and providing autofocus.

The documentation is comprehensive, non-proprietary and easy to access. It is 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 £100, orders of magnitude below commercial lab microscopes.


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 programing, 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.