Smart EPU Software

Thermo Scientific EPU 3 Software has been reimagined to allow both new and experienced microscopists to set up their experiments more quickly and easily. Features include:

• Predefined experiment templates for facilitating experiment setup
• Automatic precheck and reporting for a clearer view on the microscope status
• Automated repair of system status - available on the following cryo-TEMs: the Thermo Scientific Tundra Cryo-TEM, Glacios Cryo-TEM, and Krios Cryo-TEM
• Evolving suite of automation algorithms, – for simplifying screening and data collection (e.g., algorithm that auto-selects grid squares based on one user-selected candidate grid square)
• Intuitive user interface for smoother facilitation of new user training

EPU Multigrid Software allows users to take full advantage of their Autoloader by enabling them to setup and queue multiple data acquisition experiments to run unattended and overnight. Features include:

• Efficient microscope utilization — for less microscope idle time, with no need to switch manual grids in the middle of the night
• Faster time to data — for scheduling and running multiple single particle analysis screening sessions, either unattended or overnight
• Efficient grid screening — for setting up new and more efficient screening workflows

EPU Quality Monitor (EQM) Software analyzes and visualizes images on-the-fly, enabling users to judge image quality of running or completed acquisitions remotely. The combination of EPU Software, EQM Software, and smart plugins helps to generate high-quality results quickly and with confidence. Features of EQM Software include:

• Real-time 2D processing of data — for motion correction and contrast transfer function (CTF) calculations
• Flawless interface with smart plugins — for adjusting data collection settings automatically
• EPU setting adjustments — ability to let users immediately identify problematic acquisitions and fix or skip them
• Full integration with Thermo Scientific CryoFlow Software — our data integration platform that allows you to filter and export only quality data, expediting post-processing with the built-in multilayer filter

We have collaborated with Structura Biotechnology Inc. to develop an integrated version of CryoSPARC Live to significantly enhance efficiency of Thermo Scientific cryo-transmission electron microscopes (cryo-TEMs). This software shortens time to results by:

• Providing real-time, multi-dimensional feedback on sample quality and TEM settings

• Allowing imaging and processing parameter adjustments at any time to increase overall data quality

• Integrating with Thermo Scientific Smart EPU Software to support a growing set of automations

Embedded CryoSPARC Live is installed on microscope hardware. Our digital service team provides support through installation and maintenance, and our application specialists provide integral workflow training.

Smart Plugins either use AI-based image analysis to automate the selection of grid areas suitable for further imaging or dynamically adjust EPU Software settings based on real-time image analysis software (EPU Quality Monitor Software or Embedded CryoSPARC Live™) output. The current plugins available in the Smart EPU Software include:

• Smart Selection of Grid Squares — for a deep-learning-based selection and categorization of grid squares according to apparent size and other quality attributes.
• Smart Ice Thickness Prediction — for automated classification of foil holes depending on predicted ice thickness based on trained neural networks.
• Smart Filter — for auto selection of the best quality holes: A pretrained neural network that automatically exclude contaminated or broken holes on a grid square
• Smart Focus — for auto-focus stabilization: Uses real-time contrast transfer function (CTF) measured focus values to autocorrect defocusing in the microscope
• Smart Stage Time — for stage waiting time optimization: Uses real-time measured motion traces to adjust the stage waiting time to optimal setting
• Smart Grid Skip — for automated grid-square skipping: Uses real-time CTF output to skip grid squares that give suboptimal results

*CryoSPARC Live is a trademark of Structura Biotechnology Inc. and is used under license.

Fast set-up time with EPU Multigrid Software for more efficient microscope usage, combined with throughput- and quality-enhancing automation and real-time feedback when intervention is needed during acquisition.

The use of automation algorithms and AI-guided decisions reduces operator variability, making outcomes more predictable.

We are committed to continuously improving the EPU experience through regular software updates. Smart EPU Software is supported by our service organization and application specialists.