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<!doctype html>
<html>
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="chrome=1">
<title>Clearvolume by ClearVolume</title>
<link rel="stylesheet" href="stylesheets/styles.css">
<link rel="stylesheet" href="stylesheets/pygment_trac.css">
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<script src="//html5shiv.googlecode.com/svn/trunk/html5.js"></script>
<![endif]-->
</head>
<body>
<div class="wrapper">
<header>
<img src="./images/ClearVolumeLogo.png" alt="ClearVolume" align="center">
<div align="center">
<ul>
<li><a href="https://github.com/ClearVolume/ClearVolume/zipball/master">Download <strong>ZIP File</strong></a></li>
<li><a href="http://github.com/ClearVolume/ClearVolume/wiki">Go to <strong>WIKI</strong></a></li>
<li><a href="https://github.com/ClearVolume/ClearVolume">View On <strong>GitHub</strong></a></li>
</ul>
<div/>
</header>
<section>
<h3>
<a id="welcome-to-github-pages" class="anchor" href="#welcome-to-github-pages" aria-hidden="true"><span class="octicon octicon-link"></span></a>Welcome to ClearVolume.</h3>
<p><em>ClearVolume</em> is a real-time live 3D visualization library designed for high-end volumetric microscopes such as SPIM and DLSM microscopes. With <em>ClearVolume</em> you can see live on your screen the stacks acquired by your microscope instead of waiting for offline post-processing to give you an intuitive and comprehensive view on your data. The biologists can immediately decide whether a sample is worth imaging.
<em>ClearVolume</em> can easily be integrated into existing Java, C/C++, Python, or LabVIEW based microscope software. It has a dedicated interface to MicroManager/OpenSpim/OpenSpin control software. <em>ClearVolume</em> supports multi-channels, live 3D data streaming from remote microscopes, and uses a multi-pass Fibonacci rendering algorithm that can handle large volumes. Moreover, <em>ClearVolume</em> is integrated into the Fiji/ImageJ2/KNIME ecosystem. You can now open your stacks with <em>ClearVolume</em> from within these popular frameworks for offline viewing.
<p>
<iframe src="https://player.vimeo.com/video/129251639?title=0&byline=0&portrait=0" width="480" height="270" frameborder="0" webkitallowfullscreen mozallowfullscreen allowfullscreen></iframe>
</p>
<h3>
<a id="start" class="anchor" href="#start" aria-hidden="true"><span class="octicon octicon-link"></span></a>Getting started</h3>
<p>The main <a href="http://github.com/ClearVolume/ClearVolume/wiki
"><em>ClearVolume</em> wiki </a> is the place to start for in-depth installation instructions, documentation, examples, building guide, and more...</p>
To get started even faster please go:
<ul>
<li><a href="http://github.com/ClearVolume/clearvolume/wiki/Integration-in-LabVIEW">Here</a> if you are Microscope builder using LabView</li>
<li><a href="http://github.com/ClearVolume/clearvolume/wiki/OpenSPIM-Manual">Here</a> if you are an OpenSPIMer</li>
<li><a href="http://github.com/ClearVolume/clearvolume/wiki/Integration-in-Java">Here</a> if you are a Java coder</li>
<li><a href="http://github.com/ClearVolume/clearvolume/wiki/Integration-in-C-or-Cpp">Here</a> if you are a C/C++ coder</li>
<li><a href="http://github.com/ClearVolume/pyclearvolume">Here</a> if you are a Python coder</li>
<li><a href="http://github.com/ClearVolume/imglib2-clearvolume">Here</a> if you are a ImgLib2 user</li>
<li><a href="http://fiji.sc/ClearVolume">Here</a> if you want to see your data in 3d within FiJi/ImageJ</li>
<li><a href="http://tech.knime.org/book/clearvolume">Here</a> if you are a KNIME user</li>
</ul>
<h3>
<a id="repos" class="anchor" href="#repos" aria-hidden="true"><span class="octicon octicon-link"></span></a>Repositories</h3>
<p>
The <em>ClearVolume</em> project repositories are listed below:
</p>
<ul>
<li><a href="http://github.com/ClearVolume/clearvolume">ClearVolume Main Project repository.</a> </li>
<li><a href="http://github.com/ClearVolume/cleargl">ClearGL - Object Oriented facade API on top of OpenGL.</a> </li>
<li><a href="http://github.com/ClearVolume/clearcuda">ClearCUDA - Object Oriented facade API on top of CUDA.</a> </li>
<li><a href="http://github.com/ClearVolume/imglib2-clearvolume">ClearVolume Fiji plugin and imglib2 bridge interface.</a> </li>
<li><a href="http://github.com/ClearVolume/openspim-clearvolume">ClearVolume plugin to OpenSPIM.</a> </li>
<li><a href="http://github.com/ClearVolume/pyclearvolume">ClearVolume Python bindings and toolset.</a> </li>
</ul>
<h3>
<a id="authors" class="anchor" href="#authors" aria-hidden="true"><span class="octicon octicon-link"></span></a>Authors and Contributors</h3>
<p>The <em>ClearVolume</em> project was initiated by Loic Royer (<a href="https://github.com/royerloic" class="user-mention">@royerloic</a>) who wrote the first version, designed the core real-time rendering and streaming algorithms and wrote the bindings to C++/LabVIEW. Martin Weigert (<a href="https://github.com/maweigert" class="user-mention">@maweigert</a>) helps to maintain and improve the core rendering algorithms and wrote the OpenCL pipeline. Martin also contributed the Python bindings and tools, OpenCL and CUDA real-time 3D data processors for image quality estimation and center of mass calculation. Ulrik Günther (<a href="https://github.com/skalarproduktraum" class="user-mention">@skalarproduktraum</a>) developed and maintains the OpenSPIM integration, greatly contributed to the OpenGL backend, and improved C/C++ bindings. Florian Jug (<a href="https://github.com/fjug" class="user-mention">@fjug</a>) contributed the imagelib2 bridge, and wrote and maintains the <a href="http://fiji.sc/Fiji">Fiji</a> and <a href="http://www.knime.org">KNIME</a> plugins. Nicola Maghelli is our optics/microscope building genie whitout whom we could never have tested <em>ClearVolume</em> in realistic scenarios. </p>
<h3>
<a id="cite" class="anchor" href="#authors" aria-hidden="true"><span class="octicon octicon-link"></span></a>How to cite <em>ClearVolume</em></h3>
<p>
<b><a href="http://www.nature.com/nmeth/journal/v12/n6/full/nmeth.3372.html"> <em>ClearVolume</em> – Open-source live 3D visualization for light sheet microscopy.</a></b><br>
<i>Loic A. Royer, Martin Weigert, Ulrik Günther, Nicola Maghelli, Florian Jug, Ivo F. Sbalzarini, Eugene W. Myers </i>,
Nature Methods 12, 480–481 (2015) doi:10.1038/nmeth.3372
</p>
<h3>
<a id="Acknowledgements" class="anchor" href="#ack" aria-hidden="true"><span class="octicon octicon-link"></span></a>Affiliations</h3>
<p>The <em>ClearVolume</em> team brings together members of the <a href="http://www.mpi-cbg.de/research/research-groups/gene-myers.html">Myers</a> and
<a href="http://mosaic.mpi-cbg.de">Sbalzarini</a> labs at <a href="http://www.mpi-cbg.de">Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)</a>.</p>
<h3>
<a id="support-or-contact" class="anchor" href="#support-or-contact" aria-hidden="true"><span class="octicon octicon-link"></span></a>Contact</h3>
<p><a href="mailto:[email protected]">Send us an email</a> and we will get back to you.</p>
</section>
<footer>
<p>
<b>master branch:</b><br>
<a href="https://travis-ci.org/ClearVolume/clearvolume"><img src="http://travis-ci.org/ClearVolume/clearvolume.svg?branch=master" alt="ClearVolume Master Status" > ClearVolume</a><br>
<a href="https://travis-ci.org/ClearVolume/clearcuda"><img src="http://travis-ci.org/ClearVolume/clearcuda.svg?branch=master" alt="ClearCUDA Master Status" > ClearCUDA</a><br>
<a href="https://travis-ci.org/ClearVolume/cleargl"><img src="http://travis-ci.org/ClearVolume/cleargl.svg?branch=master" alt="ClearGL Master Status" > ClearGL</a><br>
<br>
<b>develop branch:</b><br>
<a href="https://travis-ci.org/clearvolume/ClearVolume?branch=develop"><img src="http://travis-ci.org/ClearVolume/clearvolume.svg?branch=develop" alt="ClearVolume Developp Status" > ClearVolume</a><br>
<a href="https://travis-ci.org/clearvolume/ClearCUDA?branch=develop"><img src="http://travis-ci.org/ClearVolume/clearcuda.svg?branch=develop" alt="ClearCUDA Developp Status" > ClearCUDA</a><br>
<a href="https://travis-ci.org/ClearVolume/cleargl?branch=develop"><img src="http://travis-ci.org/ClearVolume/cleargl.svg?branch=develop" alt="ClearGL Developp Status" > ClearGL</a><br>
</p>
<p>
<a href="https://waffle.io/clearvolume/clearvolume">
<img src="https://badge.waffle.io/clearvolume/clearvolume.svg?label=ready&title=Ready" alt="Waffle Status" >
</a>
</p>
<p>This project is maintained by the <a href="https://github.com/ClearVolume">ClearVolume Team</a></p>
<p><small>Hosted on GitHub Pages — Theme by <a href="https://github.com/orderedlist">orderedlist</a></small></p>
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