Team:TU-Delft/Zephyr

From 2013.igem.org

(Difference between revisions)
Line 5: Line 5:
<html>
<html>
-
<div id="tmp">
+
<div style="margin-left:30px;margin-right:30px; width:900px;float:left;">   
-
<div style="margin-top:40px;margin-left:30px;margin-right:30px; width:900px;float:left;">   
+
-
<h2 align="center">Zephyr: DIY low-cost fluorescence scanner</h2>
+
-
</div>
+
-
 
+
-
 
+
-
 
+
-
<div id="img">
+
-
        <div style="margin-top:10px;margin-left:40px;float:left;display:inline-block;"> 
+
-
<a href="https://static.igem.org/mediawiki/2013/9/90/Fotor0918123836.png
+
-
" target="_blank"><img src="https://static.igem.org/mediawiki/2013/9/90/Fotor0918123836.png"width="250px"  height="262px"/></a>
+
-
</div>
+
-
</div>
+
-
<br><br>
+
-
 
+
-
<div id="img">
+
-
<div style="margin-left:10px;margin-right:0px;width:630px;float:left;display:inline-block;"> 
+
<p align="justify">  
<p align="justify">  
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. </p>  
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. </p>  
Line 582: Line 566:
<center>
<center>
<img src="https://static.igem.org/mediawiki/2013/0/02/Figure_2_plate_C.png" width="600px" height="424px"/>
<img src="https://static.igem.org/mediawiki/2013/0/02/Figure_2_plate_C.png" width="600px" height="424px"/>
 +
<br><br><br>
Figure 2: Example of the collection of the different parts in the laser program
Figure 2: Example of the collection of the different parts in the laser program
</center>
</center>

Revision as of 16:10, 28 September 2013

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.

In addition to these filters and the mirror, you will also need a high power LED. The emission frequency of this LED should be very close to the frequency of the emission filter. Many of these LEDs are available on superbrightleds.com.

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
    

Making of the parts

In total 41 unique parts must be made out of plastic using laser cutting. These parts are dived into four categories: A to D. A are the parts of the dichroic holder including the LED holder. B are the parts of the optical holder, C are the frame parts and D are the parts that hold petridishes and the 96 well plates. In the table below the parts are listed with their name and their coding (e.g. B3).

Mechanical parts   
PMMA clear 6mm thick, 870 mm x 540 mmThe plastic for the frame1-
PMMA clear 6mm thick, 515 mm x 290 mmThe plastic for the frame1-
PMMA clear 3mm thick, 300 mm x 150 mm The plastic for the frame1-
Linear bearring 15 mm 8 mm 24 mmBearrings allowing sliding8 link 1
Pouley 30 tooths, 6 mm diameter holePouley to move the belt8 link 2
Belt 950 mm, 380 toothsDrive belt4 link 3
Axis 8MM diameter 312 mm lengthC194 link 4
Axis 8MM diameter 335 mm lengthC202 link 5
Bearring inside diameter 6 mm outer diameter 19 mm Bearrings to hold pouleys4 link 6
Fixation rings 8 mmTo fixate the axis12 link 7
SM1V10 - Ø1" SM1 Lens Tube, 1" Long External ThreadsLens tube allowing focussing1 link 8
CP4S - SM1-Threaded 30 mm Cage Plate, 4 mm ThickPlate mounting for the lens1 link 9
SM1A3 - Adapter with External SM1 Threads and Internal RMS ThreadsAdapter between different threads 1 link 10
M6 bolts x 40 mm +nuts4 to support the pouleys and 4 for the holding of the objectie plate8-
M3 bolts x 20 mm + nutsTo tightent belts to sliders8-
Black painte.g. exhaust paint1-
Heat transfer double sided tapeTo fixate the high power LED1 link 11
GlueTo fixate webcam-

Table 1: The parts to buy of the Zephyr, including dichroic parts for GFP detection.

For all these parts technical drawings are available below or bundled in this pdf. Note that these are the dimensions that result from using the laser cutting method.


Figure 1: The Individual technical drawings of the parts to make

So, how to make these parts? For laser cutting the parts to make must usually be supplied a ‘dxf’-format, this is a file containing the 2D structure of the different parts. For all the different parts these files can be found in this zip-file. These digital files can be directly sent to a company that can make them for you or a technician at a university. The three plastic plates will suffice to make all the parts according to the quantity. You will have to ask them to combine them in a smart way for you on the plate. This would look something in Figure 2.



Figure 2: Example of the collection of the different parts in the laser program

After these parts are cut, some must become black in order to

Assembly of the parts

Wiring the circuits

Arduino code, microprocessor

The Arduino controls both the LED, all the motors and communicates with the PC. Attached is the Arduino code file [link_to_arduino_file], which can be uploaded to the Arduino using the supplied software link.

Control software

Image processing

Explanation of the design

Desired specifications

Specific justifications

Results

Sensitivity and linearity

Petridish reading

Conclusions

Design in general

Resulting specifications

Discussion / Future aspirations