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biomesh3d  
Tetrahedral Mesh Generation

BioMesh3D is a tetrahedral mesh generator, that is capable
of generating multi-material quality meshes
out of segmented biomedical image data.


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Overview
Documentation
Support

Overview

BioMesh3D is a tetrahedral mesh generator, that is capable of generating multi-material quality meshes out of segmented biomedical image data. The BioMesh3D program uses a particle system to distribute nodes on the separating surfaces that separate the different materials and then uses the TetGen software package to generate a full tetrahedral mesh. BioMesh3D is currently integrated with SCIRun and uses the SCIRun system to visualize the intermediate results.

BioMesh3D Client is a light weight application that guides the user through the process of building a tetrahedral mesh based on a labelmap that the user has to provide. As the recipe for building a quality mesh requires a lot of computation, this application allows the user to connect to the Scientific Computing and Imaging Institutes' servers for doing the meshing. Hence this package only contains an interface to connect to this remote server.

Download BioMesh3D Client


BioMesh3D Acknowledgement
BioMesh3D License
CIBC Acknowledgement


Acknowledgement: BioMesh3D is an Open Source software project that is principally funded through the SCI Institute's NIH/NIGMS CIBC Center. Please use the following acknowledgment and send us references to any publications, presentations, or successful funding applications that make use of NIH/NIGMS CIBC software or data sets.

 "This project was supported by the National Institute of General Medical Sciences of the National Institutes of Health under grant number P41GM103545."

BioMesh3D Citation: [bibtex citation] [Endnote citation]




BioMesh3D and BioMesh3D Client License

BioMesh3D and BioMesh3D Client are available for free and open source under the MIT License

The MIT License Copyright (c) 2010 Scientific Computing and Imaging Institute, University of Utah. License for the specific language governing rights and limitations under Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.



NIH/NIGMS Center for Integrative Biomedical Computing Acknowledgment


CIBC software and the data sets provided on this web site are Open Source software projects that are principally funded through the SCI Institute's NIH/NIGMS CIBC SCIRun License For us to secure the funding that allows us to continue providing this software, we must have evidence of its utility. Thus we ask users of our software and data to acknowledge us in their publications and inform us of these publications. Please use the following acknowledgment and send us references to any publications, presentations, or successful funding applications that make use of the NIH/NIGMS CIBC software or data sets we provide.

"This project was supported by the National Institute of General Medical Sciences of the National Institutes of Health under grant number P41GM103545."

Documentation

Documentation for BioMesh3D can be found with the SCIRun documentation

BioMesh3D Tutorialpdf button


Support


SCIRun/BioMesh3D Mailing Lists
Reporting Bugs and Feature Requests

Joining the SCIRun Users Mailing List

  1. Compose an email to This email address is being protected from spambots. You need JavaScript enabled to view it. with the following in the body of message: subscribe scirun-users
  2. Nothing needed in the Subject line. Just send.
  3. You will receive a response from the list manager requesting confirmation. Just send back a reply message to confirm your subscription (no added text needed).
  4. Finally, you will receive a welcome message confirming that you have been added to the mailing list.

Unsubscribing

  1. Compose an email to This email address is being protected from spambots. You need JavaScript enabled to view it. with the following in the body of message: unsubscribe scirun-users
  2. Nothing needed in the Subject line. Just send.
  3. You will receive a response from the list manager notifying you that the command has succeeded and you have been removed from the list.

The same procedure should be used to subscribe to the scirun-develop mailing list.



Please send bugs and feature requests to This email address is being protected from spambots. You need JavaScript enabled to view it." rel="nofollow">This email address is being protected from spambots. You need JavaScript enabled to view it.
You must be a member of the scirun-develop mailing list to send bugs. Please follow the SCIRun Mailing Lists instructions to subscribe:
  1. Compose an email to This email address is being protected from spambots. You need JavaScript enabled to view it. with the following in the body of message: subscribe scirun-develop
  2. Nothing needed in the Subject line. Just send.
  3. You will receive a response from the list manager requesting confirmation. Just send back a reply message to confirm your subscription (no added text needed).
  4. Finally, you will receive a welcome message confirming that you have been added to the mailing list.

Developers with SCI or SCI collaborator accounts can report bugs and request features through the tracker on the SCI GForge portal.




For general questions about SCIRun, please send an email to CIBC Technical Manager (Elizabeth Jurrus): This email address is being protected from spambots. You need JavaScript enabled to view it.