Smart EPU Software for single particle analysis

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.

Key features of Smart EPU Software


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.


Professionally developed and maintained

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


On-demand webinar: Smart EPU Software

View our 45-minute webcast in which we introduce the Smart EPU ecosystem, to understand how:

  • Smart EPU Software simplifies single particle analysis data collection for easier operation, improved efficiency, and productivity.
  • EPU Quality Monitor to analyze and visualize images in real-time.
  • Smart plug-ins automatically adjust data collection settings on the fly.

Watch on-demand

Components of Smart EPU Software

  • EPU 3 Software: enables both new and experienced microscopists to set up their experiments more quickly and easier with this latest version of our EPU software.
  • EPU Multigrid Software: maximizes microscope efficiency by setting up a queue of automated acquisitions across multiple grids.
  • EPU Quality Monitor (EQM): Determine the quality of your data in real-time.
  • Embedded CryoSPARC Live:Integrated real-time data analysis to monitor image and sample quality.
  • Smart Plugins: provide on-the-fly decision algorithms that automatically adjust EPU settings based on output from real-time image analysis.
  • Open Application Programming Interface (API): allows you to develop your own customized decision algorithms and automation routines for EPU Software.

Thermo Scientific Smart EPU Software for cryo-TEM single particle data acquisition
Smart EPU Software is a single particle analysis data acquisition solution with interactive software components that automate multiple steps in acquisition, enabling advanced, and guided decision making throughout the workflow.

Software components

EPU 3 Software for 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-TEM, Glacios 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
Thermo Scientific EPU Software user interface
An embedded traffic-light UI element makes it easy to see the microscope’s status.

EPU Multigrid Software

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

Get an overview of Smart EPU Software and its components for scheduling, data acquisition, and decision algorithms.

EPU Quality Monitor

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 Athena Software, our data management platform that allows you to filter and export only quality data, expediting post-processing with the built-in multilayer filter

Smart plug-ins

Smart plug-ins either dynamically adjust EPU Software settings based on real-time image analysis software (EPU Quality Monitor Software or Embedded CryoSPARC Live^™) output; use image-based AI to suggest the operator make changes; or even make decisions in acquisition strategy. The first plugins to be released with Smart EPU Software include:

  • 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
  • Smart Select, auto selecting the best quality holes
  • A pretrained neural network that automatically selects the best holes on a grid square

Open Application Programming Interface (API)

The Smart EPU ecosystem, through its open API, allows you to develop plug-ins 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 plug-ins


Smart EPU Software deployment, services, and support

EPU Deployment


We ensure seamless integration of Smart EPU Software into your on-site environment, allowing you to optimize your infrastructure investments.

EPU Training


Our experts are dedicated to helping you shorten your learning curve to be your most productive with Smart EPU Software.

EPU Support


Our worldwide customer support team is ready to assist you and answer all your questions about Smart EPU, any time you need it.

Style Sheet for Global Design System
Style Sheet for Komodo Tabs
Style Sheet for Instrument Cards Original

Contact us

Electron microscopy services for
the life sciences

To ensure optimal system performance, we provide you access to a world-class network of field service experts, technical support, and certified spare parts.

Style Sheet for Komodo Tabs
Style Sheet to change Applications H3 to p with em-h3-header class
Style Sheet to change H3 to p with em-h3-header class
Style Sheet to change H2 style to p with em-h2-header class
Style Sheet for Support and Service footer
Style Sheet for Fonts
Style Sheet for Cards