Computer chip designers, materials scientists, biologists and other scientists now have an unprecedented level of access to the world of nanoscale materials thanks to 3D visualization software that connects directly to an electron microscope
The capabilities are included in a new version of tomviz, an open-sourced 3D data visualization tool that has already been used by tens of thousands of researchers. The new version makes it possible to go from a microscope sample to a 3D visualization in less than a day.
Researchers can see and manipulate 3D visualization during an ongoing experiment thanks to the new capabilities. It could speed up research in fields such as microprocessors, electric vehicle batteries and lightweight materials.
It has been a longstanding dream of the Semiconductor industry to be able to do tomography in a day, and here we have cut it to less than an hour. It's possible to start interpreting and doing science before you finish your experiment.
A fundamental change from previous versions of tomviz is that the new software pulls data directly from an electron microscope. Researchers used to gather data from the electron microscope, which takes hundreds of two-dimensional projection images of a nanomaterials from several different angles. It took several hours to create a 3D visualization of an object after they took the projections back to the lab. A problem with one step of the process often meant starting over.
There is a new version of tomviz. Within a few minutes, researchers can get a shadowy but useful 3D render.
You don't know what you're going to find until you see it. The ability to make adjustments while on the microscope makes a big difference in the research process.
Semiconductor chip makers could use tomography to run tests on new chip designs, looking for failures in three-dimensional circuitry far too small to see. It was too slow to run the hundreds of tests required in a commercial facility in the past.
Tomviz can be run on a laptop. Older models of electron microscopes can be connected to it. The software is open source and accessible to everyone.
It is possible to use open-source software for empowering science around the world. The connection between tomviz and the microscope was made by us. "Because the software only looks at the data from the microscope, it doesn't care if that microscope is the latest model at U-M or a twenty-year old machine."
The U-M team brought on a team of scientists who work at the intersection of data science, materials science and microscopy to help develop the new capabilities.
The idea of a version of tomviz that would enable real-time visualization and experimentation was developed at the beginning of the process. The U-M materials science and engineering graduate researcher Jonathan Schwartz and machine learning and materials science expert Yi Jiang collaborated with the developers of Hovden and Kitware to create a program that could turn electron microscopy images.
The user interface that would support the new capabilities was designed by David Muller and Peter Ericus.
A group of people, including a materials science and engineering professor, an undergraduate data scientist, a biointerfaces research fellow, and a chemical engineering research fellow, worked together to create a nanoparticles that could be used in real life. They chose a helix-shaped nanoparticles that was 100 nanometers wide and 500 nanometers long. Within minutes, the new version of tomviz generated an image that was shadowy but detailed enough for the researchers to make out key details. The shadows were resolved into a three-dimensional visualization.
The tomviz source code is free to download. It is believed that it will open new possibilities to fields other than materials-related research. He hopes the project's "software as science" approach will spur new innovation in the field of science and software development.
There is an interdisciplinary approach to research at the intersection of computer science, material science, physics, chemistry. Only you and your graduate students know how to use the cool algorithms you've created. If you can allow labs across the world to do these things, it's another thing.
Kitware collaborated with many people on the project. Cejka Professor of Engineering, and a professor of chemical engineering and macromolecule science and engineering.
Schwartz is excited for all the new science discoveries and 3D visualization that will come out of the material science and microscopy community.
More information: Jonathan Schwartz et al, Real-time 3D analysis during electron tomography using tomviz, Nature Communications (2022). DOI: 10.1038/s41467-022-32046-0 Journal information: Nature Communications
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