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| --- | ||
| # Documentation: https://sourcethemes.com/academic/docs/managing-content/ | ||
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| title: "Volume Renderer for use with MATLAB®" | ||
| summary: "GPU accelerated volume renderer for use with MATLAB®" | ||
| authors: [admin] | ||
| tags: [volume renderer, software, 3D image analysis] | ||
| categories: [Software] | ||
| date: 2012-07-14T17:09:58+01:00 | ||
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| # Optional external URL for project (replaces project detail page). | ||
| external_link: "" | ||
| external_link: https://github.com/raphiniert-com/homepage | ||
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| # Featured image | ||
| # To use, add an image named `featured.jpg/png` to your page's folder. | ||
| # Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. | ||
| image: | ||
| caption: "" | ||
| focal_point: "" | ||
| preview_only: true | ||
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| # Custom links (optional). | ||
| # Uncomment and edit lines below to show custom links. | ||
| # links: | ||
| # - name: Follow | ||
| # url: https://twitter.com | ||
| # icon_pack: fab | ||
| # icon: twitter | ||
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| url_code: "" | ||
| url_pdf: "/downloads/volumerenderer-1.0.pdf" | ||
| url_slides: "" | ||
| url_video: "" | ||
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| # Slides (optional). | ||
| # Associate this project with Markdown slides. | ||
| # Simply enter your slide deck's filename without extension. | ||
| # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. | ||
| # Otherwise, set `slides = ""`. | ||
| slides: "" | ||
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| draft: false | ||
| share: false | ||
| commentable: false | ||
| editable: false | ||
| --- | ||
| ## Features | ||
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| _Volume Renderer for use with MATLAB®_ extends MATLAB® by a GPU-accelerated volume render command that handles 3D volumetric data. The core application is implemented in C/C++. To guarantee fast computations the render process computes on the GPU. This is realized by NVIDIA® CUDA®. Furthermore _Volume Renderer <small>for use with MATLAB®</small>_ provides the following features: | ||
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| * **Special memory management:** Due to restricted GPU memory and the requirement to render more than one volume in one scene, we developed a special memory management to enable the rendering of huge data sets in separate rendering passes. Afterward these separately rendered images are combined to one image using MATLAB®. | ||
| * **Generic illumination model:** We developed a generic illumination model that is easy to extend with other illumination functions. The provided function is the Heneyey-Greenstein phase function. | ||
| * **Stereo rendering:** In some use cases there is a nice feature to work with stereo images. Thus, the renderer offers the possibility to render off-axis stereo images. | ||
| * **High usability:** To enable a high usability a MATLAB® interface consisting of several MATLAB® classes has been developed. Due to this interface it is uncomplicated to generate movies. | ||
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| More detailed explanation of the renderer and its background can be found in the documentation in the download section. We provide this software only for 64 bit Linux systems. | ||
| It was developed by Raphael Scheible supervised by Benjamin Ummenhofer and Junior-Prof Dr. Olaf Ronneberger and is maintained by Raphael Scheible. | ||
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| ## Requirements | ||
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| * CUDA® capable NVIDIA® graphics device | ||
| <small>(at least Fermi™ architecture)</small> | ||
| * Linux computer (64 bit) with installed NVIDIA® driver and CUDA® 4.2 | ||
| * MATLAB® (*) | ||
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| <small>* tested and developed under R2010a; might work from 2009a as the OOP feature was introduced the renderer uses.</small> | ||
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| ## Example | ||
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| The following video demonstrates the power of the renderer. | ||
| <small>provided by Benjamin Ummenhofer, data from [[1]](#references)</small> | ||
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| {{< youtube HdYV1dY41qw >}} | ||
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| ## Download | ||
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| * Documentation: [documentation-1.0.pdf](/static/volume-renderer/volumerenderer-1.0.pdf) | ||
| <small>md5sum: 5af53f26fe5965eb7ac9d69a2c0050be</small> | ||
| * Software: [vrm-1.0.tar.gz](/static/volume-renderer/vrm-1.0.tar.gz) | ||
| <small>md5sum: f324f09f3b7845876e5caf50a71b2f12</small> | ||
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| ## Installation | ||
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| Copy the files of src/matlab/ and bin/ into your current working folder. From this locationyou can now easily call the renderer. | ||
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| If you want to compile src/HeneyeyGreenstein.cc by yourself, use themex command in your MATLAB® environment: | ||
| **mex** _inputfile_ -output _resultname_ | ||
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| For a more detailed explanation of the mex command visit [this website](http://www.mathworks.com/help/matlab/ref/mex.html) . | ||
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| Alternatively, you can use the HG.mexa64\. This provides the command to build alookup table for the illumination setup. This is a compiled version of HeneyeyGrennstein.cc. | ||
| If you want to write your own illumination function, you can adaptHeneyeyGrennstein.cc accordingly. | ||
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| ## Licence | ||
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| The provided matlab code and C-code for building the Heneyey-Greenstein LUT are released under [New BSD License](http://opensource.org/licenses/BSD-3-Clause) . | ||
| The matlab binary files (render command and binary of Heneyey-Greenstein.h) are relesed under the following license: | ||
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| ```bash | ||
| Copyright © 2012, Raphael Scheible All rights reserved. | ||
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| Redistribution and use of the software, with or without modification, are permitted provided that | ||
| the following conditions are met: | ||
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| 1. Redistributions must reproduce the above copyright notice, this list of conditions and | ||
| the following disclaimer in the documentation and/or other materials provided with the distribution. | ||
| 2. No names of contributors may be used to endorse or promote products derivedfrom this | ||
| software without specific prior written permission. | ||
| 3. The project has to be non-commercial in which this softare is used. | ||
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| THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR | ||
| IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY | ||
| AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR | ||
| CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL | ||
| DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, | ||
| DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, | ||
| WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) | ||
| ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | ||
| ``` | ||
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| ## Contact | ||
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| Feel free to contact [Raphael Scheible](/#contact) with questions and issues. If you find a bug, please report it. | ||
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| ### Using _Volume Renderer <small>for use with MATLAB®</small>_ ? | ||
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| Please let me know if you are using _Volume Renderer <small>for use with MATLAB®</small>_ as I am interested in how it is used in other research works. | ||
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| ## Acknowledgments | ||
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| _Volume Renderer <small>for use with MATLAB®</small>_ was developed as a student project by Raphael Scheible at University of Freiburg supervised by [Benjamin Ummenhofer](http://lmb.informatik.uni-freiburg.de/people/ummenhof/) and [Junior-Prof. Dr. Olaf Ronneberger](http://lmb.informatik.uni-freiburg.de/people/ronneber/) . | ||
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| ## References | ||
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| 1. <a name="ref1"></a>Ronneberger, O and Liu, K and Rath, M and Ruess, D and Mueller, T and Skibbe, H and Drayer, B and Schmidt, T and Filippi, A and Nitschke, R and Brox, T and Burkhardt, H and Driever, W. **[ViBE-Z: A Framework for 3D Virtual Colocalization Analysis in Zebrafish Larval Brains](http://lmb.informatik.uni-freiburg.de//Publications/2012/RLSDSBB12) .** 2012. _Nature Methods,_ 9(7):735--742. | ||
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| caption: GitHub project page | ||
| focal_point: Smart | ||
| --- |