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Why software matters in cryo-EM
Thermo Scientific cryo-EM software orchestrates cryo-EM workflows—from automated data acquisition to 3D reconstruction, correlation, management, and visualization. Fully integrated into our cryo-TEM, cryo-FIB, and volume EM instruments, these software platforms can help you simplify complex processes, generate high-quality data faster, and scale operations with confidence.
Which cryo-EM software do you need?
Whether you’re focused on single particle analysis (SPA), cryo-electron tomography (Cryo-ET), or volumetric imaging, our software ecosystem delivers the automation, accuracy, and connectivity needed to transform raw data into breakthrough results.
This table highlights the differences between programs and how they can support your workflows.
| Workflow stage | Recommended software | How it helps |
|---|---|---|
| CLEM sample setup and targeting | Maps Software | Correlates optical and EM data for precise targeting. |
| SPA acquisition and analysis | Smart EPU Software | Automates the single particle analysis workflow with AI-driven tools for fast feedback on image and sample quality. |
| Cryo-ET acquisition and analysis | CryoTomo Software Suite | Automates tilt-series collection and 3D reconstruction for fast feedback on sample quality. |
| Cryo-EM data management | CryoFlow Software | Centralizes remote and secured access to cryo-EM datasets in a single environment for easy collaboration. |
| Volume-EM | Auto Slice & View 5 Software | Automates serial block-face imaging for 3D reconstruction. |
| Visualization and analysis | Amira Software | Visualizes, segments, and interprets complex 3D datasets. |
CryoFlow Software
Integrated data management for cryo-EM workflows
Thermo Scientific CryoFlow Software seamlessly connects to Smart EPU Software for single particle analysis workflows and the CryoTomo Software Suite for cryo-ET workflows, providing data organization, reporting, and automatic, instant data transfer. Compatible with Thermo Scientific Glacios, Krios, and Tundra Cryo-TEMs, CryoFlow Software accelerates your research and ensures your results are reproducible, traceable, and ready for analysis.
Smart EPU Software with Embedded CryoSPARC Live
Intelligent data collection for efficient single particle analysis
Thermo Scientific™ Smart EPU™ Software automates grid screening and data collection for single particle analysis workflows. Compatible with Thermo Scientific™ Cryo-TEMs, it combines AI-driven automation, multigrid support, and real-time image quality monitoring to deliver consistent, high-quality datasets with minimal setup. Integrated with CryoSPARC™ Live and enabled by Thermo Scientific™ CryoFlow™ Software, Smart EPU Software accelerates 3D model generation for faster, more productive single particle analysis workflows.
CryoTomo Software Suite
Integrated data acquisition and analysis for cryo‑ET
Designed to bring a highly efficient cryo-ET workflow to both new and experienced users, the Thermo Scientific CryoTomo Software Suite provides integrated tools that streamline tilt series acquisition and 3D analysis. Available for Thermo Scientific Cryo-TEMs, the suite is powered by Thermo Scientific Tomography 5 Software with multigrid support and Tomo Live Software for real-time data quality monitoring and curation. These tools work natively with CryoFlow Software for specialized visualization and data management.
Maps Software
Correlative targeting for multimodal cryo-EM imaging
Thermo Scientific Maps Software precisely aligns optical and electron microscopy data to help you identify and target regions of interest with sub-micrometer accuracy. It integrates the data with both Thermo Scientific microscopes and third-party systems, supporting workflows where sample context is critical, such as cell biology, neuroscience, and structural studies. By connecting multimodal datasets into a single platform, it enhances confidence in data collection and accelerates the path to discovery.
Amira Software
3D visualization and analysis for cryo-EM datasets
Thermo Scientific Amira Software provides advanced 3D visualization, segmentation, and quantitative analysis tools for cryo-EM and volume EM datasets. It can help you reconstruct volumes, identify structures, and extract quantitative measurements to generate meaningful biological insights. Its intuitive interface and customizable workflows support both detailed exploration and large-scale studies, transforming raw image data into interpretable results.
Auto Slice & View Software
Volume-EM acquisition for high-resolution 3D imaging
Thermo Scientific Auto Slice & View 5 Software automates serial block-face imaging for high-resolution volumetric electron microscopy, controlling both ion beam milling and electron beam imaging. It removes the need for manual intervention during the imaging process while supporting high-throughput acquisition of large 3D datasets. Its integration with Thermo Scientific FIB-SEMs ensures streamlined operation to help reveal structural details and spatial relationships that were previously difficult to access.
Explore cryo-EM software updates and releases
For Research Use Only. Not for use in diagnostic procedures.