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

Abstract

Three-dimensional characterization of materials at the nano- and meso-scale has become possible with transmission and scanning transmission electron microscopes (S/TEM). Its importance has extended to a wide class of nanomaterials such 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 instead tailored for lower-dose, biological applications and not optimized for higher-resolution materials applications. Existing tomography fails to utilize the chemical information provided by S/TEM spectrometers. To address this problem, this project delivered a scalable, fully functional, freely-distributable, open Source materials tomography package with a modern user interface that enables automated acquisition, alignment, and real-time reconstruction of raw tomography data, and provides advanced segmentation, three-dimensional chemical visualization and analysis optimized for materials applications. It has established an extendable framework capable of automation for high-throughput for the tomography of materials from data acquisition to visualization. Phase I and II delivered a full-featured, cross-platform, clean and integrated application for S/TEM materials tomography. It can read projection data from the microscope, with graphical tools for alignment of data, tomographic reconstruction, segmentation, and visualization of the reconstructed 3D volume. The entire pipeline can be saved to an XML state file, enabling fully reproducible data processing and analysis with a full Python environment for the development of custom algorithms, processing, and analysis requirements. Phase IIB extended the application to provide real-time tomographic reconstruction, "live updates" as data is processed, analysis of big data, and multi-channel tomography. Here, quantitative assessment of nanomaterials can occur as data is being recorded on a 3D visualization platform that accommodates additional information from multiple channels. We provide unmatched high-throughput tomography, where the complete tomographic pipeline from measurement to 3D visualization can occur rapidly. The project was extended to offer capabilities for micro-CT, X-ray, neutron, focused ion beam, atomic electron tomography and atom probe tomography. With over 600 transmission electron microscopes worldwide and 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 enhance three-dimensional imaging at the nanoscale and bring automated high-throughput approaches that will accelerate progress in materials characterization and metrology. The project supports a service based business model by enabling lab-specific acquisition and processing customization and integration-support and development that will be provided into Phase III and beyond.