Open-Source Visualization and Analysis Platform for 3D Reconstructions of Materials by Transmission Electron Microscopy

Three-dimensional characterization of materials at the nano- and meso-scale has become possible with transmission and scanning transmission electron microscopes. Its importance has extended to a wide class of nanomaterialssuch as hydrogen fuel cells, solar cells, industrial catalysts, new battery materials and semiconductor devices, as well as spanning high-tech industry, universities, and national labs. While capable instrumentation is abundant, this rapidly expanding demand for high-resolution tomography is bottlenecked by software that is tailored for lower-dose, biological applications and not optimized for higher-resolution materials applications. To address this problem, Phase I of this proposal will deliver a fully functional, freely-distributable, open-source scanning transmission electron microscopy tomography package with a modern user in- terface that enables alignment and reconstruction of raw tomography data, and provides advanced three-dimensional visualization and analysis optimized for materials applications. It will establish an extendable framework which will position the Phase II project to focus on full automation for high-throughput electron tomography of materials from data acquisition to visualization. The Phase I approach will combine empirically-tested tomography strategies with professional software interfaces to develop a clean and fully integrated application for 3D visualization and reconstruction. This user-friendly, cross-platform, graphical desktop application will read trans- mission electron microscope image data, provide graphical tools to perform user-assisted alignment of images collected on the instrument, and sophisticated analysis of the resulting volumetric re- constructed data. Within the application, an interface will allow user-developed reconstruction algorithms to be fully integrated into the workflow. In addition to providing significantly en- hanced, intuitive software, the application will enable reproducible workflows where the full path of data from collection to final analyzed results can be saved and shared. With around 600 transmission electron microscopes worldwide and a growth of approximately 50 coming online each year, the demand and impact of an open-source tomography tool is large. Significant opportunities exist in high-tech industry, universities, and national labs to enable or en- hance three-dimensional imaging at the nanoscale and bring automated high-throughput approaches that will accelerate progress in materials characterization and metrology. The project will support a service based business model by enabling services-based consulting, technology integration and customizationsupport and development that will be provided into Phase III.