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

 
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             <h1>Microscopy Server</h1>
 
             <h1>Microscopy Server</h1>
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<h3>Turn your Raspberry Pi into a web-accessible microscope.</h3><p>Look and control your microscope from your computer, phone, table or with a monitor connected to the Pi itself. Find out about the architecture of our web stack here.</p></div></div></section>
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<h3>Turn your Raspberry Pi into a web-accessible microscope.</h3><p>Look and control your microscope from your computer, phone, table or with a monitor connected to the Pi itself. You can connect to the microscope just like another computer over SFTP. After installing WinSCP (Windows) or Cyberduck (Mac) or Nautilus (Linux), it is easy to connect to the Pi (default username: pi, password: raspberry). Download your images as if they were on another folder.</p>
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<p>Our software runs on nginx, a widely used lightweight web server. Behind this, we run an image streamer (<a href="https://github.com/moosd/mjpg-streamer" class="blue">mjpg-streamer</a>) and our own python scripts. nginx deals with the user control and load balancing, leaving us to implement the various features of our microscope.</p><center><a href="http://github.com/sourtin/igem15-sw/" class="btn btn-default btn-lg" style="color:#444;border-color:#444"><i class="fa fa-github"></i>Visit our github</a><br><br><a href="//2015.igem.org/wiki/images/f/fe/CamJIC-Dist-OpenScope-Utilities.zip" class="btn btn-default btn-lg" style="color:#444;border-color:#444"><i class="fa fa-download"></i>Download source code (frozen from wiki freeze)</a><br><br><a href="//2015.igem.org/images/Cambridge-JIC-NOOBSCOPE.zip" class="btn btn-default btn-lg" style="color:#444;border-color:#444"><i class="fa fa-download"></i>Download our prepared SD card</a></center><br>
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<center><p>For more detailed installation instruction, visit the <a href="https://2015.igem.org/Team:Cambridge-JIC/Downloads#Software" class="blue">Downloads</a> page.</p></center>
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        <a class="btn btn-default btn-lg" href="//2015.igem.org/Team:Cambridge-JIC/Autofocus" role="button" style="color:#1b4f18;border-color:#b1e7ad">Learn More</a>
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            <h1>Webshell</h1>
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<h3>Microscopy in a nutshell.</h3><p>Everything you expect from a standard microscope. And more. WebShell shows the live stream from the microscope, while allowing control over the light sources and motorised axes. Apply sample recognition algorithms with opencv. Measure your cells by dragging a line across. Set up timelapses. Control it all from the keyboard like a video game. #gamifyingmicroscopy</p></div></div></section>
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        <p><b>Crisp, sharp images every time.</p></b><p>Focusing on samples manually can be difficult. <b>OpenScope supports autofocus</b>. Find out more about the algorithms we used and see how they compare.</p>
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            <h1>ImageJ</h1>
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        <a class="btn btn-default btn-lg" href="//2015.igem.org/Team:Cambridge-JIC/Webshell" role="button" style="color:#3d3d3d;border-color:#3d3d3d">Learn More</a>
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<h3>OpenScope integrates with your favourite image processing tool.</h3><p>For many years, scientists have used ImageJ to process microscope images. Our ImageJ plugin allows you to remotely connect to the microscope, see the live view, control the microscope lights and motors, while also letting you take pictures and import them straight into ImageJ. One click, no hassle.</p>
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      <p><b>Microscopy in a nutshell:</b> Everything you expect from a standard microscope. And more.</p><br> <p style="text-align:right">Live stream from the microscope<br>Control the light sources and the motorised axes<br>Sample recognition algorithms with OpenCV<br>Measurements and scalebars<br>Timelapses</p></div>
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<p>Keyboard control - like a video game.</p>        </div></div>
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        <a class="btn btn-default btn-lg" href="//2015.igem.org/Team:Cambridge-JIC/MicroMaps" role="button" style="color:#1b4f18;border-color:#1b4f18">Learn More</a>
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<h3>Crisp, sharp images every time.</h3><p>Focusing on samples is typically very fiddly. OpenScope supports autofocus. Find out more about the algorithms we used and see how they compare.</p>
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        <p><b>Never get lost on your slide again.</b> MicroMaps performs image stitching in the background, allowing you to navigate your slide, just like exploring an online map.</p>
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        <a class="btn btn-default btn-lg" href="//2015.igem.org/Team:Cambridge-JIC/ImageJ" role="button" style="color:#123a68;border-color:#123a68">Learn More</a>
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<h3>Never get lost on your slide again.</h3><p>MicroMaps performs image stitching in the background, allowing you to navigate your slide, just like exploring an online map.</p>
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<div style="right:4%;left:70%;top:15%;font-size:20px;position:absolute;color:#123a68">
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      <p><b>OpenScope integrates with your favourite image processing tool.</b></p>
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<div style="left:4%;right:40%;top:33%;font-size:20px;position:absolute;color:#123a68">
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<p>For many years, scientists have used ImageJ for image processing. Our ImageJ plugin allows you to remotely connect to  and control OpenScope, while also letting you take pictures and import them straight into ImageJ.</div>
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<div style="left:4%;right:40%;top:85%;font-size:20px;position:absolute;color:#123a68"><b>One click, no hassle.</b></p>
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Latest revision as of 22:55, 18 September 2015

CAMBRIDGE-JIC

Microscopy Server

Turn your Raspberry Pi into a web-accessible microscope.

Look and control your microscope from your computer, phone, table or with a monitor connected to the Pi itself. You can connect to the microscope just like another computer over SFTP. After installing WinSCP (Windows) or Cyberduck (Mac) or Nautilus (Linux), it is easy to connect to the Pi (default username: pi, password: raspberry). Download your images as if they were on another folder.

Our software runs on nginx, a widely used lightweight web server. Behind this, we run an image streamer (mjpg-streamer) and our own python scripts. nginx deals with the user control and load balancing, leaving us to implement the various features of our microscope.

Visit our github

Download source code (frozen from wiki freeze)

Download our prepared SD card

For more detailed installation instruction, visit the Downloads page.

Crisp, sharp images every time.

Focusing on samples manually can be difficult. OpenScope supports autofocus. Find out more about the algorithms we used and see how they compare.

Microscopy in a nutshell: Everything you expect from a standard microscope. And more.


Live stream from the microscope
Control the light sources and the motorised axes
Sample recognition algorithms with OpenCV
Measurements and scalebars
Timelapses

Keyboard control - like a video game.

Never get lost on your slide again. MicroMaps performs image stitching in the background, allowing you to navigate your slide, just like exploring an online map.

OpenScope integrates with your favourite image processing tool.

For many years, scientists have used ImageJ for image processing. Our ImageJ plugin allows you to remotely connect to and control OpenScope, while also letting you take pictures and import them straight into ImageJ.

One click, no hassle.