Single particle analysis cryo-EM data acquisition software

Single particle cryo-electron microscopy (cryo-EM) uses the particles extracted from thousands of images to reconstruct 3D structures of macromolecules. The yield of an acquisition session at the microscope depends on the time needed to set up the run and the speed of the acquisition itself. Thermo Scientific Smart EPU Software is an innovative, easy-to-use data acquisition solution for single particle analysis that focuses on automation and user guidance to increase throughput and deliver reproducible results. Available on all our transmission electron microscopy (TEM) platforms, Smart EPU Software allows you to focus more on your research and make efficient use of your microscope.


Smart EPU Software is an ecosystem of multiple interactive software components that work together to drive automation of the data acquisition steps. The software enables advanced AI-guided decisions.

Smart EPU Software features

EPU 3 Software for cryo-EM data acquisition

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 to facilitate experiment setup
  • Automatic precheck and reporting of microscope status with clear visual indications
  • Automated repair of system status available on the following cryo-TEMs: the Thermo Scientific Tundra Cryo-TEMGlacios Cryo-TEM, and Krios Cryo-TEM
  • Evolving suite of automation algorithms, simplifying screening and data collection e.g., algorithm that auto-selects grid squares based on one user-selected candidate grid square
  • Intuitive user interface, which facilitates training of new users

EPU Multigrid Software for Autoloader equipped instruments

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 Software

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 — motion correction and CTF calculations
  • Flawless interface with smart plugins to adjust data collection settings automatically
  • Ability to let users immediately identify problematic acquisitions and fix or skip them by EPU setting adjustments
  • 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

Embedded CryoSPARC Live Software

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). Embedded CryoSPARC Live significantly shortens time to results by providing real-time, multi-dimensional feedback on sample quality and transmission electron microscope settings. It allows you to adjust imaging and processing parameters at any time, increasing overall data quality and minimizing time wasted on poor quality samples. And it fully integrates with Thermo Scientific Smart EPU Software via CryoFlow 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 EPU Software Plugins

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.

Open Application Programming Interface (API)

The Smart EPU ecosystem, through its open API, allows you to develop plugins that interact with Smart EPU Software. User-developed plugins can take advantage of artificial intelligence/machine learning to evaluate microscope output and adjust microscope settings on the fly.

  • Sharing among the cryo-EM community: open API allows the broader community to share their own do-it-yourself (DIY) plugins
  • Customize and develop your own plugins

Smart EPU Software benefits for single particle analysis

Ease of use

EPU presets, microscope traffic lights, and smart automation benefit from artificial intelligence that captures the decisions of cryo-EM specialists in its algorithms.

Higher throughput

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.

Continuous innovation and application support

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.

Smart EPU Software tutorials

Smart EPU Software webinars