Cross platform, open source application for the processing, visualization, and analysis of 3D tomography data
![tomviz_logo]
The [Tomviz project][tomviz] is developing a cross platform, open source application for the processing, visualization, and analysis of 3D tomographic data. It features a complete pipeline capable processing data from alignment, reconstruction, and segmentation through to displaying, visualizing, and interacting with 3D reconstructions of tomographic data. Many of the data operators are available as editable Python scripts that can be modified in the interface to experiment with different techniques. The pipeline can be saved to disk, and a number of common file formats are supported for importing and exporting data.
![tomviz_screenshot]
The Tomviz project was founded by [Marcus D. Hanwell][Hanwell] and [Utkarsh Ayachit][Ayachit] at [Kitware][Kitware], [David A. Muller][Muller] ([Cornell University][Cornell]), and [Robert Hovden][Hovden] ([University of Michigan][Michigan]), funded by DOE Office of Science contract DE-SC0011385.
Installing
Tomviz is currently undergoing major upgrades. Updated packages are available on conda-forge for Linux:
conda install -c conda-forge tomviz
Within the next 6 months, we plan to provide conda-forge packages for all other operating systems (Windows, macOS), as well as installable binary packages (MSI, DMG, etc.).
Older releases
For older releases, we recommend downloading the stable release. Nightly binaries were also previously built by our [dashboards][Dashboard] for Windows, macOS, and Linux.
Windows: Follow the installation instructions, double-click on the Tomviz icon to launch the application. macOS: After downloading the package double-click to begin installation. Drag the Tomviz icon into your Applications directory – or anywhere else you would like to store it. Double-click on the icon to open it, nightly builds will require right-clicking and selecting open. Linux: A binary (tar.gz) is provided, or it can be built from source. See instructions for building found in the BUILDING.md document.
A Quick Tutorial
1. Open a sample dataset by clicking “Sample Menu > Reconstruction ” at the top menubar. 2. Create a 3D volumetric visualization by clicking “Visualization > Volume” at the top menubar. 3. Interact with your volume in the center panel titled “RenderView”.
User Guide
Start by watching this short video to [see Tomviz in action][tomvizinaction].
Also Tomviz user guide has more detailed information to get started.
Cite Tomviz
When using tomviz in your research, please cite:
Publications using Tomviz
- A Simple Preparation Method for Full-Range Electron Tomography of Nanoparticles and Fine Powders, E. Padgett et al., Microsc. & Microanalys. (2017)
- Physical Confinement Promoting Formation of Cu2O–Au Heterostructures with Au Nanoparticles Entrapped within Crystalline Cu2O Nanorods, E. Asenath-Smith et al., Chem. Mater. (2017)
- Nanomaterial datasets to advance tomography in scanning transmission electron
Our project uses GitHub for code review, please fork the project and make a pull request if you would like us to consider your patch for inclusion.
![Kitware, Inc.][KitwareLogo]
[tomviz]: https://tomviz.org/ "The Tomviz project" [tomviz_logo]: https://github.com/OpenChemistry/tomviz/blob/master/tomviz/icons/tomvizfull.png "tomviz" [tomvizscreenshot]: https://github.com/OpenChemistry/tomviz/blob/master/docs/images/screencapmacwidev0.6.0.gif "tomviz screenshot v0.6.0" [tomvizinaction]: https://vimeo.com/189945022 "Tomviz in action" [Kitware]: http://kitware.com/ "Kitware, Inc." [KitwareLogo]: http://www.kitware.com/img/smalllogoover.png "Kitware" [Cornell]: http://www.aep.cornell.edu/ [Michigan]: http://www.engin.umich.edu/ [Hanwell]: http://www.kitware.com/company/team/hanwell.html [Ayachit]: http://www.kitware.com/company/team/ayachit.html [Muller]: http://muller.research.engineering.cornell.edu/ [Hovden]: http://www.roberthovden.com/ [Dashboard]: http://open.cdash.org/index.php?project=tomviz "tomviz dashboard"
