Kitware Receives Funding to Develop Open-Source S/TEM Materials Reconstruction Software in Partnership with Cornell University Researchers

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Application will help scientific community meet growing demand for improved S/TEM microscopy software for visualization and analysis of nanoscale materials.

In Phase II, the team will develop an extendable, turn-key platform that is capable of fully-automated, high-throughput electron tomography of nanoscale materials.

Kitware has announced Phase II funding from the Department of Energy (DoE) to continue development of an open-source platform for materials reconstruction using scanning transmission electron microscopes (S/TEM), in partnership with researchers at Cornell University.

The project is a response to shortcomings in current state-of-the-art tomography software processes that involve long analysis cycle times and the use of several different file formats, which makes it difficult to document and publish analysis and reconstruction results in a manner that is accessible to the broader scientific community. Motivated to provide a solution, Kitware is collaborating with Cornell University to build tomviz, a fully-functional, freely-distributable S/TEM platform that provides advanced segmentation, three-dimensional (3D) visualization, and analysis optimized for materials applications.

“There are approximately 600 transmission electron microscopes in the world today, and close to 50 new microscopes are made available online each year, creating a high demand for an open-source tomography platform,” Dr. Robert Hovden, a postdoctoral researcher at Cornell University and key collaborator on the project, said.

During Phase I, the team produced a cross-platform application that reads transmission electron microscope image data, implements graphical tools for user-assisted data alignment, performs basic tomographic reconstruction, and visualizes the resulting 3D volume. The application has already been well-received, with hundreds of downloads from the scientific community.

“The application presents users with advanced, intuitive software and workflows that enable the full path of data from collection to final, analyzed results to be saved, shared, and even published as supporting information,” Dr. Marcus D. Hanwell, the Principal Investigator for the project and a Technical Leader at Kitware, said.

In Phase II, the team will develop an extendable, turn-key platform that is capable of fully-automated, high-throughput electron tomography of nanoscale materials. The platform will feature a modern user interface and enhanced graphical tools for editing, aligning, segmenting, visualizing, and analyzing data. It will also feature one-click tomography, making it possible to easily reconstruct experimental data and visualize it in 3D.

“As a result of the project, it will be possible to have the entire tomography process, from measurement to 3D analysis, take place on a single graphical platform,” Hanwell said. “This technology will greatly accelerate progress in materials characterization and metrology, while also promoting reproducible science.”

To learn more about Kitware’s HPC and visualization expertise, and how it can be used to your organization’s advantage, please contact kitware(at)kitware(dot)com.

This material is based upon work supported by the Department of Energy under 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.

About Kitware
Kitware is an advanced technology, research, and open-source solutions provider for research facilities, government institutions, and corporations worldwide. Founded in 1998, Kitware specializes in research and development in the areas of HPC and visualization, medical imaging, computer vision, data and analytics, and quality software process. Among its services, Kitware offers consulting and support for high-quality software solutions. Kitware is headquartered in Clifton Park, NY, with offices in Carrboro, NC; Santa Fe, NM; and Lyon, France. More information can be found on

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