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

Period of Performance: 04/06/2015 - 04/05/2017


Phase 2 SBIR

Recipient Firm

28 Corporate Drive Array
Clifton Park, NY 12065
Firm POC
Principal Investigator


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 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. To address this problem, this proposal will deliver a fully functional, freely-distributable, open- source scanning transmission electron microscopy tomography package with a modern user inter- face that enables automated acquisition, alignment, and reconstruction of raw tomography data, and provides advanced segmentation, three-dimensional visualization and analysis optimized for materials applications. It will establish an extendable framework capable of full automation for high-throughput electron tomography of materials from data acquisition to visualization. Phase I combined empirically-tested tomography strategies with professional software interfaces to develop a clean and integrated application for 3D visualization and reconstruction. The cross- platform application can read transmission electron microscope image data, provides graphical tools for user-assisted alignment of data, performs basic tomographic reconstruction, and visualizes the resulting 3D volume. Within the application, an interface enables integration of advanced reconstruction and data processing routines into the work ow|providing the foundation for Phase II capabilities. Phase II will implement advanced automated alignment and reconstruction routines, along with enhanced graphical tools to edit, align, segment, visualize and analyze the reconstructed data. Support for automated data acquisition, with manual override capability, will be added to o er a turn-key fully automated work ow. Support for saving the full application work ow will o er reproducible, auditable, advanced data collection, reconstruction and analysis capabilities, supporting the call for reproducible science with data publication. With around 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 will support a service based business model by enabling lab-speci c acquisition and processing customization and integration|support and development that will be provided into Phase III.