Kitware and Collaborators Make 1.0 Release of Materials Tomography Platform

March 30, 2017

Team offers software through open-source download.

Kitware worked with researchers to make the first major release of Tomviz, an open-source platform that processes data for materials tomography. Tomviz aligns, reconstructs, segments, visualizes and analyzes three-dimensional tomographic data through a reproducible pipeline.

The release followed the conclusion of Phase II of a Department of Energy Small Business Innovation Research project. For the project, Kitware partnered with Cornell University and collaborated with members of other academic institutions to develop a multithreaded application architecture and an extensive Python environment in the platform.

“We created a responsive, graphical solution that processes and analyzes complex scientific data in a manner that may otherwise span multiple applications and programming environments,” said Marcus Hanwell, a technical leader at Kitware. Hanwell is a member of the Tomviz development team who served as the principal investigator on the project.

Tomviz shows an animation of a nanotube from Robert Hovden.

Tomviz comes ready for download as open-source binaries for major operating systems like Windows, macOS and Linux. To begin the pipeline, Tomviz imports projection images from transmission electron microscopes in industry-standard file formats such as Tagged Image File Format (TIFF), Medical Research Council (MRC) and Electron Microscopy Datasets (EMD). While the platform can automatically align these images, it enables users to manually adjust the tilt and rotation of the axis.

“Throughout the pipeline, Tomviz remains highly interactive,” said Robert Hovden, a former postdoctoral researcher at Cornell University and a founder of the Tomviz development team. “Tomviz runs data operators in background threads, so users can continue to work with the platform while it executes operations.”

The platform builds on the capabilities of the Insight Segmentation and Registration Toolkit, the Visualization Toolkit and ParaView. Through hardware-accelerated rendering techniques, for example, Tomviz lets users alter visualization parameters such as the opacity, lighting, color and orientation of volumes and geometries. Tomviz not only provides different rendering modes, but it contains multiple tools for analysis. One tool, a ruler, measures the lengths of objects in images. Tomviz also computes surface area, volume and other labeled object attributes, which it displays in a spreadsheet that users can save.

In addition to tabular data, Tomviz allows users to save its state with all data pipeline settings. Users can share and modify these settings to help others follow the necessary steps to reproduce results. Tomviz saves results as movies or exports them on the web as HTML files. To foster open dissemination, the Tomviz development team made live examples publicly available on GitHub. These examples utilize images or the latest Web Graphics Library (WebGL) rendering techniques.

Kitware offers services to support Tomviz. Through these services, users can work with Kitware experts to add features to or customize the platform. For more information, please contact kitware(at)kitware(dot)com.

This material is based upon work supported by the Department of Energy under Office of Science Award Number DE-SC0011385.

This report was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agency thereof, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof.

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