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

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<center><h4> Camera Specifications </h4>
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<tr><td>pixel size:</td><td>1.4&mu;mx1.4&mu;m</td></tr>
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<tr><td>sensor size:</td><td>2592x1944 pixels</td></tr>
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<tr><td>total:</td><td>5MP</td></tr>
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<tr><td>focal length:</td><td>3.6mm</td></tr>
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<tr><td>aperture:</td><td>1.25mm</td></tr>
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<a href="https://www.raspberrypi.org/documentation/hardware/camera.md" class="blue"> Source: Raspberry Pi </a></center>
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<h1 style="line-height:1.295em">Resolution Assessment of a Microscope Based on a Raspberry Pi Camera</h1>
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<h3>Theory of Optics</h3>
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<p> The resolution can be limited by two independent factors: </p> <ul><li><p>pixel size;</p></li><li><p>diffraction effects.</p></li></ul>
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<div style="float:left"> <img src="//2015.igem.org/wiki/images/8/8b/CamJIC-Resolution.jpg" style="height:280px;margin:20px"> </div> <p> The larger of these determines the actual limitation of the system. In our case we know that the pixel size is 1.4 &mu;m, so we now need to work out the diffraction limit, that is the smallest spot size which can be produced by the lens with the given specs. To calculate this, recall the Rayleigh criterion for a circular aperture: sin&theta;=1.22 &lambda;/d. Here &lambda;~550nm is the wavelength of light, taking green for the middle of the visible spectrum, d=1.25mm is the diameter of the aperture and &theta; (small angle) is the angular radius of the spot, that is tan&theta;=r/L. Here r is the radius of the spot projected at a distance L from the aperture, which in our setup is actually the focal length f of the Raspberry Pi camera lens (and the spot is projected onto the CCD sensor). <br> <br> <br>
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From first approximation for a small angle: sin&theta;=tan&theta;, so 1.22 &lambda;/d=r/f. Rearranging this equation and plugging in the numbers gives the following diameter of the smallest resolvable spot: 2r=3.8&mu;m. This is almost three times the size of the pixel on the CCD, which imposes the actual limit on the resolution. The pixels of the CCD outresolve the theoretical lens limits.</p>
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<p><center><h4 style="padding:2em 0"> Final resolution estimate of a microscope based on Raspberry Pi camera: 3.8&mu;m </h4> </center></p>
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<div style="float:right"> <img src="//2015.igem.org/wiki/images/7/78/CamJIC-SpirogyraZoomIn.png" style="height:200px;margin:20px"> </div>
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<p> Compare this with a typical size of a chloroplast: 5-8&mu;m diameter [1]. Our resolution will be just enough to image them, which is exactly what we have managed to do on this picture of Spirogyra cells. Note that these are larger than typical chloroplasts though. To obtain a better resolution, a lens with either larger aperture and/or shorter focal distance can be used, without the need of a better CCD. However, this is a tradeoff in terms of worse aberration and contrast. An improvement to the resolution will however be required in order to image bacteria, for example, which are of the order of 1&mu;m in diameter [2].</p>
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<p style="font-size:80%"> [1] Wise, R. and Hoober, J. (2006). The structure and function of plastids. Dordrecht: Springer. <br> [2] Encyclopedia Britannica, (2015). bacteria :: Diversity of structure of bacteria. <a href="http://www.britannica.com/science/bacteria/Diversity-of-structure-of-bacteria" class="blue">[online]</a> [Accessed 30 Jul. 2015].</p>  
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<h3> Inverting the Lens: Why and How </h3>
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<p>The way a camera works is by focusing an image of a distant large object as a small set of points onto the CCD, which is positioned close to the lens (in its focal plane). Theoretically however, it might as well do the opposite (because light paths are reversible – a well known and intuitive physical principle): that is, inspect the CCD pixels and project their greatly enlarged image onto a distant screen. <br>The lens has a small aperture (1.25mm) at one end, and a larger one (4mm) offering a wider view angle at the other, which is required for viewing close up objects. This is normally oriented towards the CCD. <br> </p> <center> <img src="//2015.igem.org/wiki/images/a/a2/CamJIC-CameraDiagram.JPG" style="height:250px;margin:20px"> <img src="//2015.igem.org/wiki/images/6/64/CamJIC-MicroscopeDiagram.JPG" style="height:250px;margin:20px"> </center>
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<br><p>So, if we want to image a sample on a microscope slide, we need to:</p><ul>
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<li><p>position the lens close to the sample – at roughly the focal distance, that is 3.6mm;</p></li>
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<li><p>orient the lens with its larger aperture towards the sample;</p></li>
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<li><p>position the sensor behind the lens, now at a much larger distance (roughly 2.8cm) – for this we have designed a special camera mount.</p></li></ul>
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<p>Now we have the Raspberry Pi camera working as a microscope!</p>
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<p><b>The problem: how to unscrew the lens from the camera</b>
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The Raspberry Pi camera is sold with the lens screwed (and lightly glued) into the sensor casing. To unscrew the lens, you will need the right type of pliers: ideally with ridged surface. Grip the top part of the plastic casing of the lens firmly, being careful not to crush it, and rotate counterclockwise.  After the first small rotation, you should be able to unscrew it fully manually. <i>ATTENTION: might not work from the first time! Do not try to cut out the lens or force it out in any other way.</i>
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            <h2>Abstract</h2>
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            <p>Fluorescence microscopy has become a ubiquitous part of biological research and synthetic biology, but hardware can often be <span class="hl_1">large and prohibitively expensive</span>. 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 <span class="hl_1">laborious and time-consuming</span> than it needs to be.</p>
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          <p>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 <span class="hl_1">well documented, physically compact, easily modifiable and high quality fluorescence microscope</span> 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.</p>
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<h1 style="line-height:1.295em"> Power Consumption Assessment </h1>
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<h3> OpenScope Power Consumption </h3>
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<p style="font-size: 120%"> Below is a table of the components of our microscope (equivalent for fluorescence and brightfield modes). A typical 8hr day is used for comparison, and the data for the 3D printer is also included for completeness. However, this will of course only be used during assembly and is not included in the running consumption.
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<p>The mechanics of the microscope will be 3D printable, and all other parts will be cheap and accessible. These introduce a novel method (developed by Dr Richard Bowman, Cambridge) for <span class="hl_2">precise positioning and control</span> which exploits the flexibility of the printed parts. The microscope will also utilise the developed-in-Cambridge Raspberry Pi board and camera module for image capture. Ultimately we are aiming for <span class="hl_2">4 micron resolution</span>, both in brightfield and fluorescence modes.</p>
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          <p>Furthermore, software used to control commercial microscopes is very much focused upon translating the physical experience of using a microscope into a computer. We aim to leverage the full computational potential of a digital microscope, <span class="hl_2">carefully considering functional UX design</span> to allow control (locally and also over a network) via a Google Maps-like interface and implementing <span class="hl_2">background image processing</span>, <span class="hl_2">annotation</span> and <span class="hl_2">stitching</span>, as well as allowing <span class="hl_2">fully autonomous operation</span>.</p>
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     <th class="tg-031e">Component<br></th>
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    <th class="tg-031e">Power per unit / W<br></th>
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    <th class="tg-031e">kWh/day for 8hr use</th>
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    <td class="tg-031e">Raspberry Pi Model B [1]</td>
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    <td class="tg-031e">4.0 *</td>
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    <td class="tg-031e">0.032</td>
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    <td class="tg-031e">20mA LEDs x5 [2]</td>
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    <td class="tg-031e">0.10 **</td>
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    <td class="tg-031e">0.004</td>
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    <td class="tg-031e">Servo Motors x2</td>
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    <td class="tg-031e">7.0 **</td>
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    <td class="tg-031e">0.11</td>
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    <td class="tg-031e">22" LCD Monitor</td>
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    <td class="tg-031e">30 **</td>
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    <td class="tg-031e">0.24</td>
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    <td class="tg-031e">Arduino Uno [3]</td>
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    <td class="tg-031e">0.25 ***</td>
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    <td class="tg-031e">0.004</td>
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    <td class="tg-031e" colspan="2"><center><b>TOTAL</b></center></td>
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    <td class="tg-031e"><b>0.39</b></td>
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    <td class="tg-031e">3D Printer (Ultimaker 2) [4]</td>
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    <td class="tg-031e">220 **</td>
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    <td class="tg-031e">1.8</td>
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<p style="font-size:80%"> * Based on 900MHz quad-core ARM Cortex-A7 CPU <br>** Numerous models with different characteristics. Values given represent the appliances we’ve used<br>*** Based on ATmega328 processor</p>
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<h3> Commercial Microscope Consumption</h3>
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<p style="font-size: 120%"> This data is provided for comparison:</p>
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    <th class="tg-031e">Component<br></th>
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    <th class="tg-031e">Power per unit, W<br></th>
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    <td class="tg-031e">HBO 100 Mercury lamp [5]</td>
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    <td class="tg-031e">100 *</td>
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    <td class="tg-031e">0.80</td>
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    <td class="tg-031e">Tungsten-Halogen lamp [5]</td>
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    <td class="tg-031e">100 *</td>
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    <td class="tg-031e">0.80</td>
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    <td class="tg-031e">XBO 75 Xenon arc lamp [5]</td>
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    <td class="tg-031e">75 *</td>
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    <td class="tg-031e">0.60</td>
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<p style="font-size:80%">* Most commonly used lamp wattages according to ZEISS Microscopy Online Campus</p>
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<p style="font-size: 120%"> Note: Relevant equations for power consumption estimates and unit conversion (Recall your high school physics!)</p> <ul><li> <p>Conversion from W to kWh/day for 8 hour use:  E<sub>(kWh/day)</sub>=P<sub>(W)</sub>&times;t<sub>(h/day)</sub>/1000<sub>(W/kW)</sub></p></li><li> <p>Conversion to W from A (based on 5V DC standard power supply from USB port): P<sub>(W)</sub>=I<sub>(A)</sub>&times;U<sub>(V)</sub></p></li></ul>
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<p style="font-size:80%"> [1]  Raspberry Pi, (2015). Raspberry Pi 2 Model B. <a href="https://www.raspberrypi.org/products/raspberry-pi-2-model-b/" class="red">[online]</a>   [Accessed 30 Jul. 2015]. <br> [2] RS Components UK, (2015). Lighting | RS Components. <a href="http://uk.rs-online.com/web/c/lighting/" class="red">[online]</a> [Accessed 31 Jul. 2015]. <br> [3] Arduino.cc, (2015). Arduino - ArduinoBoardUno. <a href="https://www.arduino.cc/en/Main/arduinoBoardUno" class="red">[online]</a> [Accessed 30 Jul. 2015]. <br> [4] Ultimaker.com, (2015). Ultimaker 2 | Ultimaker. <a href="https://ultimaker.com/en/products/ultimaker-2-family/ultimaker-2" class="red">[online]</a> [Accessed 30 Jul. 2015].<br> [5] Zeiss-campus.magnet.fsu.edu, (2015). ZEISS Microscopy Online Campus <a href="http://zeiss-campus.magnet.fsu.edu/articles/lightsources/powertable.html" class="red">[online]</a> [Accessed 30 Jul. 2015]. </p>
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Revision as of 16:10, 3 August 2015

CAMBRIDGE-JIC

Abstract

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, physically compact, easily modifiable and high quality 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.

The mechanics of the microscope will be 3D printable, and all other parts will be cheap and accessible. These introduce a novel method (developed by Dr Richard Bowman, Cambridge) for precise positioning and control which exploits the flexibility of the printed parts. The microscope will also utilise the developed-in-Cambridge Raspberry Pi board and camera module for image capture. Ultimately we are aiming for 4 micron resolution, both in brightfield and fluorescence modes.

Furthermore, software used to control commercial microscopes is very much focused upon translating the physical experience of using a microscope into a computer. 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.