Difference between revisions of "Team:Cambridge-JIC/Make Your Own"

 
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<p>We are dedicated to making the OpenScope easy to assemble and use, even for the inexperienced user. We have put together a detailed instruction and compressed all 3d-printable designs into a single archive.</p>
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<center><p>We are dedicated to making the OpenScope easy to assemble and use, even for the inexperienced user. We have put together a detailed instruction and compressed all 3d-printable designs into a single archive. Get started with OpenScope.</p></center>
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<center><a class="btn btn-default" href="" role="button" style="color:#444;border-color:#fff;;margin:10px">instructions</a><a class="btn btn-default" href="//2015.igem.org/wiki/images/d/d5/CamJIC-OpenScope.zip" role="button" style="color:#444;border-color:#fff;margin:10px">printables</a></center>
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<center><img src="https://static.igem.org/mediawiki/2015/8/81/CamJIC-gallery12.jpeg" style="width:500px;margin:10px"></center>
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<center><a class="btn btn-default" href="//2015.igem.org/wiki/images/5/57/CamJIC-MYO.pdf" role="button" style="color:#444;border-color:#fff;margin:10px">instructions</a><a class="btn btn-default" href="//2015.igem.org/wiki/images/d/d5/CamJIC-OpenScope.zip" role="button" style="color:#444;border-color:#fff;margin:10px">printables</a><a class="btn btn-default" href="//2015.igem.org/wiki/images/d/d0/CamJIC-OpenScope-BOM.pdf" role="button" style="color:#444;border-color:#444;margin:10px">bill of materials</a></center>
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<center><p>For software installation instructions, and tips on using the Raspberry Pi, visit the <a href="//2015.igem.org/Team:Cambridge-JIC/Downloads#Software" class="blue">Software Downloads</a> section.</p></center>
 
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         </video>
 
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         <p>Assemble the OpenScope optics<hr>Having problems seeing the video above? Download the video <a href="//2015.igem.org/wiki/images/7/78/CamJIC-Video-Epicube.mp4" class="blue">here</a>.</p>
 
         <p>Assemble the OpenScope optics<hr>Having problems seeing the video above? Download the video <a href="//2015.igem.org/wiki/images/7/78/CamJIC-Video-Epicube.mp4" class="blue">here</a>.</p>
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        <p>Using the OpenScope<hr>Having problems seeing the video above? Download the video <a href="//2015.igem.org/wiki/images/0/06/CamJIC-Video-Demonstration.mp4" class="blue">here</a>.</p>
 
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Bright-field is the simplest of all imaging modes: just the sample, backlit by a white light source (LED). Bright-field microscopy does not give very good contrast, so it works best for stained samples, or intrinsically colourful samples.
 
Bright-field is the simplest of all imaging modes: just the sample, backlit by a white light source (LED). Bright-field microscopy does not give very good contrast, so it works best for stained samples, or intrinsically colourful samples.
 
<br>For unstained samples, dark-field microscopy gives better contrast. The dark-field set-up is very similar to that of bight-field, but with the addition of a dark disc (what we call the dark-field tube) in between the white light and the sample. This stops direct illumination from reaching the objective, and so the only recorded light is that scattered by the sample. The main issue with dark-field is that it gives images with very low light levels.<br>
 
<br>For unstained samples, dark-field microscopy gives better contrast. The dark-field set-up is very similar to that of bight-field, but with the addition of a dark disc (what we call the dark-field tube) in between the white light and the sample. This stops direct illumination from reaching the objective, and so the only recorded light is that scattered by the sample. The main issue with dark-field is that it gives images with very low light levels.<br>
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And, finally, fluorescence microscopy allows the imaging of fluorescent proteins (FPs). When excited by light of a specific wavelength (the excitation wavelength), these proteins emit light at a different wavelength (the emission wavelength). Each FP has its own excitation and emission wavelengths. This is why, for each specific FP you will need different LEDs for illumination and different filter sets. For a more detailed explanation on how fluorescence works, refer to our <a href="//2015.igem.org/Team:Cambridge-JIC/Modeling" class="blue">Modeling</a> page.</p>
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And, finally, fluorescence microscopy allows the imaging of fluorescent proteins (FPs). When excited by light of a specific wavelength (the excitation wavelength), these proteins emit light at a different wavelength (the emission wavelength). Each FP has its own excitation and emission wavelengths. This is why, for each specific FP you will need different LEDs for illumination and different filter sets. For a more detailed explanation on how fluorescence works, and how to pick the filters, refer to our <a href="//2015.igem.org/Team:Cambridge-JIC/Modeling" class="blue">Modeling</a> page.</p>
 
<p><b>How do I set up my 3D printer?</b><br>
 
<p><b>How do I set up my 3D printer?</b><br>
 
You will need to print your parts using PLA filament. Check out our <a href="//2015.igem.org/Team:Cambridge-JIC/3D_Printing" class="blue">3D printing guide</a>.</p>
 
You will need to print your parts using PLA filament. Check out our <a href="//2015.igem.org/Team:Cambridge-JIC/3D_Printing" class="blue">3D printing guide</a>.</p>
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<p><b>What are STL and SCAD files?</b><br>
 
<p><b>What are STL and SCAD files?</b><br>
 
If you want to view a 3D object, you will need the STL file. Use your 3D printer's own software, or download OpenSCAD. If you want to edit one of these objects, open the SCAD file and edit it using OpenSCAD. For printing, the STL file is sufficient.</p>
 
If you want to view a 3D object, you will need the STL file. Use your 3D printer's own software, or download OpenSCAD. If you want to edit one of these objects, open the SCAD file and edit it using OpenSCAD. For printing, the STL file is sufficient.</p>
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<p><b>GFP is great, but I want to image another fluorescent protein. Which LEDs do I use? What about the dichroic mirror and the excitation and emission filters?</b><br>
 
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First of all, figure out the excitation and emission wavelengths of the FP you want to image. You will want to find an LED which emits light at the excitation wavelength of the FP. LEDs emit light at a range of wavelengths - make sure that the peak wavelength of the LED is close to the excitation wavelength of the FP. For guidance on picking the filters, see our <a href="//2015.igem.org/Team:Cambridge-JIC/Modeling" class="blue">Modeling</a> page.</p>
 
  
 
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<a rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/"><img alt="Creative Commons Licence" style="border-width:0" src="https://i.creativecommons.org/l/by-sa/4.0/88x31.png" /></a><br /><span xmlns:dct="http://purl.org/dc/terms/" property="dct:title">Open Scope Documentation</span> by <a xmlns:cc="http://creativecommons.org/ns#" href="//2015.igem.org/Team:Cambridge-JIC" property="cc:attributionName" rel="cc:attributionURL" style="color:#1b4f18;">Simon Swan, Katerina Naydenova, </a> <a href="//www.phy.cam.ac.uk/people/rwb27" style="color:#1b4f18;">Richard Bowman</a> is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/" style="color:#1b4f18;">Creative Commons Attribution-ShareAlike 4.0 International License</a>. Please note that all contributions to 2015.igem.org are considered to be released under the Creative Commons Attribution.
 
<a rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/"><img alt="Creative Commons Licence" style="border-width:0" src="https://i.creativecommons.org/l/by-sa/4.0/88x31.png" /></a><br /><span xmlns:dct="http://purl.org/dc/terms/" property="dct:title">Open Scope Documentation</span> by <a xmlns:cc="http://creativecommons.org/ns#" href="//2015.igem.org/Team:Cambridge-JIC" property="cc:attributionName" rel="cc:attributionURL" style="color:#1b4f18;">Simon Swan, Katerina Naydenova, </a> <a href="//www.phy.cam.ac.uk/people/rwb27" style="color:#1b4f18;">Richard Bowman</a> is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/" style="color:#1b4f18;">Creative Commons Attribution-ShareAlike 4.0 International License</a>. Please note that all contributions to 2015.igem.org are considered to be released under the Creative Commons Attribution.
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Latest revision as of 03:41, 19 September 2015

CAMBRIDGE-JIC

Make Your Own OpenScope

If you want to make your very own OpenScope, this is the page for you!

We are dedicated to making the OpenScope easy to assemble and use, even for the inexperienced user. We have put together a detailed instruction and compressed all 3d-printable designs into a single archive. Get started with OpenScope.

instructionsprintablesbill of materials

For software installation instructions, and tips on using the Raspberry Pi, visit the Software Downloads section.

Video Tutorials

Assemble the OpenScope chassis

Having problems seeing the video above? Download the video here.

Assemble the OpenScope optics

Having problems seeing the video above? Download the video here.

Using the OpenScope

Having problems seeing the video above? Download the video here.

FAQs

What’s the difference between manual and motorised modes?
The microscope has 3 knobs: two of them are used to pan across the sample, and one is used to focus. In manual mode, these knobs are controlled by hand. In motorised mode, they are instead connected to stepper motors. This enables you to program your own panning/focusing routines, and to operate the OpenScope remotely: e.g. when it is in an incubator, or in a different lab.

What is the difference between bright-field, dark-field and fluorescence modes?
Bright-field is the simplest of all imaging modes: just the sample, backlit by a white light source (LED). Bright-field microscopy does not give very good contrast, so it works best for stained samples, or intrinsically colourful samples.
For unstained samples, dark-field microscopy gives better contrast. The dark-field set-up is very similar to that of bight-field, but with the addition of a dark disc (what we call the dark-field tube) in between the white light and the sample. This stops direct illumination from reaching the objective, and so the only recorded light is that scattered by the sample. The main issue with dark-field is that it gives images with very low light levels.
And, finally, fluorescence microscopy allows the imaging of fluorescent proteins (FPs). When excited by light of a specific wavelength (the excitation wavelength), these proteins emit light at a different wavelength (the emission wavelength). Each FP has its own excitation and emission wavelengths. This is why, for each specific FP you will need different LEDs for illumination and different filter sets. For a more detailed explanation on how fluorescence works, and how to pick the filters, refer to our Modeling page.

How do I set up my 3D printer?
You will need to print your parts using PLA filament. Check out our 3D printing guide.

What if I don’t have a 3D printer?
You can send the files from the archive to a local 3D-printing service and they will ship you the printed parts.

What are STL and SCAD files?
If you want to view a 3D object, you will need the STL file. Use your 3D printer's own software, or download OpenSCAD. If you want to edit one of these objects, open the SCAD file and edit it using OpenSCAD. For printing, the STL file is sufficient.

Creative Commons Licence
Open Scope Documentation by Simon Swan, Katerina Naydenova, Richard Bowman is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License. Please note that all contributions to 2015.igem.org are considered to be released under the Creative Commons Attribution.