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architecture.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<meta http-equiv="X-UA-Compatible" content="ie=edge" />
<link rel="icon" href="img/favicon.ico" type="image/gif" sizes="16x16" />
<link
rel="stylesheet"
href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/css/bootstrap.min.css"
integrity="sha384-MCw98/SFnGE8fJT3GXwEOngsV7Zt27NXFoaoApmYm81iuXoPkFOJwJ8ERdknLPMO"
crossorigin="anonymous"
/>
<script
src="https://code.jquery.com/jquery-3.3.1.slim.min.js"
integrity="sha384-q8i/X+965DzO0rT7abK41JStQIAqVgRVzpbzo5smXKp4YfRvH+8abtTE1Pi6jizo"
crossorigin="anonymous"
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<script
src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.14.3/umd/popper.min.js"
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crossorigin="anonymous"
></script>
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src="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/js/bootstrap.min.js"
integrity="sha384-ChfqqxuZUCnJSK3+MXmPNIyE6ZbWh2IMqE241rYiqJxyMiZ6OW/JmZQ5stwEULTy"
crossorigin="anonymous"
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<link rel="preconnect" href="https://fonts.gstatic.com" />
<link
href="https://fonts.googleapis.com/css2?family=Poppins:ital,wght@0,400;0,500;0,600;0,700;0,800;0,900;1,300;1,400;1,500;1,600;1,700;1,800;1,900&display=swap"
rel="stylesheet"
/>
<title>caMicroscope</title>
<!--
Timeless Template
(stolen from)
http://www.templatemo.com/tm-517-timeless
-->
<!-- load CSS -->
<link
rel="stylesheet"
href="https://fonts.googleapis.com/css?family=Open+Sans:300,400"
/>
<!-- Google web font "Open Sans" -->
<link rel="stylesheet" href="css/bootstrap.min.css" />
<link rel="stylesheet" href="css/style.css" />
<!-- https://getbootstrap.com/ -->
<!-- <link rel="stylesheet" href="css/templatemo-style.css" /> -->
<!-- Templatemo style -->
</head>
<body style="background-color: #fcfcfc">
<nav class="navbar">
<div class="container">
<a href="./index.html" class="nav-logo logo__color">caMicroscope</a>
<ul class="nav-menu">
<li class="nav-item">
<a href="https://wolf.cci.emory.edu/camic_org/apps/viewer/viewer.html?slideId=6452b9c306fce90019f5f447" target="_blank" class="nav-link">Live Demo</a>
</li>
<li class="nav-item">
<a href="http://camicroscope.github.io/docs" class="nav-link">Documentation</a>
</li>
<li class="nav-item">
<a href="./contributing.html" class="nav-link">Contributing</a>
</li>
<li class="nav-item">
<a href="./community.html" class="nav-link">Community</a>
</li>
<li class="nav-item">
<a href="./architecture.html" class="nav-link">Architecture</a>
</li>
<li class="nav-item">
<a
href="https://github.com/caMicroscope"
class="nav-link"
>Github</a
>
</li>
</ul>
<div class="hamburger">
<span class="bar"></span>
<span class="bar"></span>
<span class="bar"></span>
</div>
</div>
</nav>
<section class="architecture">
<div class="section__header__main" id="features">
<p>
Overview of
<span class="logo__color">caMicroscope's architecture.</span>
</p>
<p class="section__content__main">
caMicroscope is a series of services organized in a <a href="https://github.com/camicroscope/Distro/blob/master/caMicroscope.yml">docker-compose file</a> or kubernetes deployment. </br>
</br>
Most data is stored in <b>mongo</b> by default in a database named "camic".</br>
The image data is stored in the filesystem and tiles are served by the <b>iip</b> microservice <a href="https://github.com/camicroscope/iipImage" target="_blank">(source).</a></br>
WSI metadata extraction is accomplished both as a service and as a series of scripts by the <b>loader</b> service <a href="https://github.com/camicroscope/SlideLoader" target="_blank">(source).</a></br>
A special version of the orthanc <b>dicom server</b> may be used to load DICOM images as well <a href="https://github.com/camicroscope/dicomsrv" target="_blank">(source).</a></br>
The API microservice, proxying to the other services, and basic security are handled by the backend <b>caracal</b> service <a href="https://github.com/camicroscope/caracal" target="_blank">(source).</a><br/>
Finally, the <b>viewer</b> is also hosted by caracal, and handles user interaction, and is the core of the project <a href="https://github.com/camicroscope/caMicroscope" target="_blank">(source).</a><br/>
</p>
<p class="section__content__main">
See the component map to understand these services in more detail.
<div id="componentMap" style="width: 500px; height:500px;">
</div>
</p>
</div>
</section>
<div style="width:100%; height:5px; background-color:#d720e1"></div>
<div style="width:100%; height:12px; background-color:#9a2ca0"></div>
<div class="footer-container">
<div class="footer-content">
<img src="img/CamicLogo.svg" class="logo" style="width:100px; height:100px;" />
</div>
<div class="footer__content__copyright"></div>
</div>
<script src="/js/navbar-responsive.js"></script>
<script src="/js/footer.js"></script>
<script src="https://cdn.jsdelivr.net/npm/openseadragon@4.1/build/openseadragon/openseadragon.min.js"></script>
<script type="text/javascript">
OpenSeadragon({
id: "componentMap",
prefixUrl: "https://cdn.jsdelivr.net/npm/openseadragon@4.1/build/openseadragon/images/",
tileSources: {
type: 'image',
url: '/img/componentMap.png'
}
});
</script>
</body>
</html>