Team:TU-Delft/Zephyr

From 2013.igem.org

(Difference between revisions)
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<h2 align="center">Part list
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<h2 align="center">Part list</h2>
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</h2>
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<p align="justify">
 +
In Table 1 the parts are listed into three categories: optical-, electrical- and mechanical components with a possible online store to buy the components. The plastic PMMA sheets are difficult to acquire online, it usually works the best to contact a local plastic supplier. Most of the mechanical parts can be swapped out for ones with the same dimensions, e.g. the bearings.
 +
</p>
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 +
<p align="justify">
 +
Note that in this list only dichroic parts for GFP are listed, for other wavelengths other parts are necessary. The dichroic parts are the excitation- and emission filter and the dichroic mirror itself. For many fluorescent proteins <a href=”http://www.edmundoptics.com/optics/optical-filters/bandpass-filters/pre-mounted-fluorescence-filter-cubes/3611" target="blank">Edmund Optics</a> has listed a good choice for these. If your fluorescent protein is not on there, the following guidelines may help you: Find out the emission frequency of your protein, pick the frequency of the 25 mm emission filter as close as possible. Pick the dichroic 25.2 x 35.6mm mirror 20 nm lower than this frequency and the 25 mm excitation filter 40 nm lower than the emission filter.
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</style><table class="tableizer-table">
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<tr class="tableizer-firstrow"><th>Code</th><th>Name</th><th>Material [B/C]</th><th>Thickness [mm]</th><th>Quantity</th></tr>
 +
<tr><td>A1</td><td>Dichroic bottom</td><td>B</td><td>5</td><td>2</td></tr>
 +
<tr><td>A2</td><td>Dichroic side ort 1</td><td>B</td><td>5</td><td>1</td></tr>
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<tr><td>A3</td><td>Dichroic side ort 2</td><td>B</td><td>5</td><td>1</td></tr>
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<tr><td>A4</td><td>Dichroic ort exc filter</td><td>B</td><td>5</td><td>1</td></tr>
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<tr><td>A5</td><td>Dichroic below emm.filter</td><td>B</td><td>3</td><td>1</td></tr>
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<tr><td>A6</td><td>Dichroic after emm. filter</td><td>B</td><td>5</td><td>1</td></tr>
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<tr><td>A7</td><td>Dichroic before exc. filter</td><td>B</td><td>5</td><td>1</td></tr>
 +
<tr><td>A8</td><td>Dichroic holder</td><td>B</td><td>5</td><td>2</td></tr>
 +
<tr><td>A9</td><td>Dichroic LED side 1</td><td>B</td><td>5</td><td>1</td></tr>
 +
<tr><td>A10</td><td>Dichroic LED end</td><td>B</td><td>5</td><td>1</td></tr>
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<tr><td>A11</td><td>Dichroic LED side 1</td><td>B</td><td>5</td><td>1</td></tr>
 +
<tr><td>B1</td><td>Holder side</td><td>B</td><td>5</td><td>2</td></tr>
 +
<tr><td>B2</td><td>Holder side LED</td><td>B</td><td>5</td><td>1</td></tr>
 +
<tr><td>B3</td><td>Holder front (bottom)</td><td>B</td><td>5</td><td>1</td></tr>
 +
<tr><td>B4</td><td>Holder front (middle)</td><td>B</td><td>5</td><td>1</td></tr>
 +
<tr><td>B5</td><td>Holder front (top)</td><td>B</td><td>5</td><td>1</td></tr>
 +
<tr><td>B6</td><td>Holder bottom</td><td>B</td><td>5</td><td>1</td></tr>
 +
<tr><td>B7</td><td>Holder dichroic</td><td>B</td><td>5</td><td>2</td></tr>
 +
<tr><td>B8</td><td>Eyepiece holder bottom</td><td>B</td><td>5</td><td>1</td></tr>
 +
<tr><td>B9</td><td>Eyepiece holder top</td><td>B</td><td>5</td><td>1</td></tr>
 +
<tr><td>B10</td><td>Objective holder plate</td><td>B</td><td>5</td><td>1</td></tr>
 +
<tr><td>C1</td><td>Frame bottom</td><td>C</td><td>5</td><td>1</td></tr>
 +
<tr><td>C3</td><td>Frame step side</td><td>C</td><td>5</td><td>4</td></tr>
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<tr><td>C4</td><td>Frame axis low</td><td>C</td><td>5</td><td>4</td></tr>
 +
<tr><td>C5</td><td>Frame high axis</td><td>C</td><td>5</td><td>4</td></tr>
 +
<tr><td>C6</td><td>Frame pouley side</td><td>C</td><td>5</td><td>4</td></tr>
 +
<tr><td>C7</td><td>Frame top</td><td>C</td><td>5</td><td>1</td></tr>
 +
<tr><td>C8</td><td>Frame arduino bottom</td><td>C</td><td>5</td><td>1</td></tr>
 +
<tr><td>C9</td><td>Frame arduino side</td><td>C</td><td>5</td><td>2</td></tr>
 +
<tr><td>C10</td><td>Frame arduino end</td><td>C</td><td>5</td><td>2</td></tr>
 +
<tr><td>C11</td><td>Slider orthogonal</td><td>C</td><td>5</td><td>12</td></tr>
 +
<tr><td>C12</td><td>Slider par. inside</td><td>C</td><td>5</td><td>4</td></tr>
 +
<tr><td>C13</td><td>Slider par. outside</td><td>C</td><td>5</td><td>4</td></tr>
 +
<tr><td>C14</td><td>Slider top</td><td>C</td><td>5</td><td>12</td></tr>
 +
<tr><td>C15</td><td>Belt connector</td><td>C</td><td>5</td><td>2</td></tr>
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<tr><td>C16</td><td>Low slider parallel</td><td>C</td><td>5</td><td>4</td></tr>
 +
<tr><td>C17</td><td>High slider orthogonal</td><td>C</td><td>5</td><td>4</td></tr>
 +
<tr><td>C18</td><td>High slider parrallel</td><td>C</td><td>5</td><td>4</td></tr>
 +
<tr><td>C19</td><td>Slide axis</td><td>C</td><td>-</td><td>4</td></tr>
 +
<tr><td>C20</td><td>Slide beam</td><td>C</td><td>-</td><td>2</td></tr>
 +
<tr><td>D1</td><td>Carrier bottom</td><td>C</td><td>5</td><td>1</td></tr>
 +
<tr><td>D2</td><td>Carrier petridish</td><td>C</td><td>3</td><td>1</td></tr>
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<tr><td>D3</td><td>Carrier 96well</td><td>C</td><td>3</td><td>1</td></tr>
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<tr><td>D4</td><td>Carrier minipetr.</td><td>C</td><td>3</td><td>1</td></tr>
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<tr><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td></td></tr>
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</table>
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Revision as of 14:14, 28 September 2013

Zephyr: DIY low-cost fluorescence scanner



Zephyr is a low-cost Do It Yourself (DIY) machine which can scan petridishes and 96 well plates for expression of fluorescence at micrometer scale. The Typhoon is the commercial machine that does the same, only it is priced around 120.000 dollars. The main difference is the use of low-cost optics. This allows you to pick exactly which fluorescence you want to detect and not to pay for the ones you do not use. Furthermore, it does not have confocal optics, as this is not that often when scanning bacteria and protein gels. This DIY machine can be built by anyone with one or two days on their hands and the costs are around 1500 dollars.

  Figure 1: The way to Zephyr! Joep in action!


Why? Reason d’être

Research is not cheap in general and synthetic biology is no exception. Much of the lab equipment has a price running of ten thousand dollars. For some teams this is no hurdle, their lab has all the equipment they possibly may need, while other teams may struggle with their characterization because of lack of needed equipment. This may be an explanation why in the iGEM competition For most of the mentioned equipment, only the high tech versions are available, which make it so costly. However the simple versions of these machines would be enough in most cases. As an analog: there are only high tech Bentleys available and no Ford Fiestas, while these Fiestas would be enough for simple transportation.

Therefore we decided to build a low-cost Typhoon, which would be easy to make on your own. This machine is of course not as high-tech as the Typhoon, but it measures at the same scale and has roughly the same performance.

What? Working principle

How? The Zephyr DIY guide Overview

Part list

In Table 1 the parts are listed into three categories: optical-, electrical- and mechanical components with a possible online store to buy the components. The plastic PMMA sheets are difficult to acquire online, it usually works the best to contact a local plastic supplier. Most of the mechanical parts can be swapped out for ones with the same dimensions, e.g. the bearings.

Note that in this list only dichroic parts for GFP are listed, for other wavelengths other parts are necessary. The dichroic parts are the excitation- and emission filter and the dichroic mirror itself. For many fluorescent proteins Edmund Optics has listed a good choice for these. If your fluorescent protein is not on there, the following guidelines may help you: Find out the emission frequency of your protein, pick the frequency of the 25 mm emission filter as close as possible. Pick the dichroic 25.2 x 35.6mm mirror 20 nm lower than this frequency and the 25 mm excitation filter 40 nm lower than the emission filter.

CodeNameMaterial [B/C]Thickness [mm]Quantity
A1Dichroic bottomB52
A2Dichroic side ort 1B51
A3Dichroic side ort 2B51
A4Dichroic ort exc filterB51
A5Dichroic below emm.filterB31
A6Dichroic after emm. filterB51
A7Dichroic before exc. filterB51
A8Dichroic holderB52
A9Dichroic LED side 1B51
A10Dichroic LED endB51
A11Dichroic LED side 1B51
B1Holder sideB52
B2Holder side LEDB51
B3Holder front (bottom)B51
B4Holder front (middle)B51
B5Holder front (top)B51
B6Holder bottomB51
B7Holder dichroicB52
B8Eyepiece holder bottomB51
B9Eyepiece holder topB51
B10Objective holder plateB51
C1Frame bottomC51
C3Frame step sideC54
C4Frame axis lowC54
C5Frame high axisC54
C6Frame pouley sideC54
C7Frame topC51
C8Frame arduino bottomC51
C9Frame arduino sideC52
C10Frame arduino endC52
C11Slider orthogonalC512
C12Slider par. insideC54
C13Slider par. outsideC54
C14Slider topC512
C15Belt connectorC52
C16Low slider parallelC54
C17High slider orthogonalC54
C18High slider parrallelC54
C19Slide axisC-4
C20Slide beamC-2
D1Carrier bottomC51
D2Carrier petridishC31
D3Carrier 96wellC31
D4Carrier minipetr.C31
    

Drawings