Powerful, automated solution for 3D cryo-electron tomography data acquisition software

Cryo-electron tomography (Cryo-ET) is a high-resolution technique that enables you to image a cell’s molecular machinery at physiological conditions. The in situ capabilities of cryo-electron tomography allow it to bridge the gap between single particle analysis (SPA) and structural cell biology, linking molecular insights to cellular behavior. Thermo Scientific Tomography 5 Software brings you the latest advances in cryo-electron tomography, allowing you to acquire valuable 3D data, even on your most challenging vitrified samples. Its new user-friendly interface enables both experienced and new users to jumpstart their tomography data acquisition.

Tomography 5 Software benefits

Reduced learning curve

Reduced learning curve with step-by-step set-up of tomographic data acquisition.

High-throughput 3D-data acquisition

Robust feature-of-interest tracking during tilting in multi-shot tomography.

Fast setup

Intuitive features help you set up regions for analysis and offer a range of imaging presets.

Tomography 5 Software features

Automatic cassette mapping

Automatic cassette mapping delivers grid quality assessment and lamella identification. Map up to 12 grids stored in the cryo-TEM autoloader system. A low-magnification map of each grid is taken, allowing for grid quality assessment and efficient. A low-magnification map of each grid is taken, allowing for grid quality assessment and efficient screening for cryo-lamella regions.

Search Maps acquisition

Maps are sets of tiles using medium magnification that enable the mapping of entire grid squares or lamellae. This leads to increased data-collection throughput and improved navigation accuracy.

Multi-site batch tomography

Multi-site batch tomography for automated, 3D data acquisition, ensuring optimal cryo-transmission electron microscope (cryo-TEM) capacity. Navigate to several regions of interest and set up tomograms, which are automatically acquired. The fully automated data acquisition runs as soon as all settings are defined.

Off-axis Multi-shot acquisition

Off-axis Multi-shot acquisition significantly enhances throughput. This feature allows several tomogram positions to be recorded with only one focus and tracking area, thereby streamlining the data acquisition process and increasing efficiency.

Dose symmetric acquisition scheme

Dose symmetric acquisition scheme ensures optimal electron dose distribution for high resolution sub-tomogram averaging. During a tomographic tilt series, the acquisition scheme exposes the projections in the lower negative and positive angular tilt range uniformly, preserving high-resolution information. This collection scheme optimizes resolution (i.e., the sub-nanometer range) and provides considerably better results than continuous or bi-directional tilt schemes.

Selectris Imaging Filter enabled

The Thermo Scientific Selectris X Imaging Filter greatly improves the signal-to-noise ratio (SNR) in tomography, boosting contrast and resolution through zero-loss filtering (i.e. the removal of inelastically scattered electrons). The imaging filter is fully integrated with Tomography 5 Software.

Cryo-electron tomography automation with Tomo Live Software

Thermo Scientific Tomo Live Software is an optional add-on for Tomography 5 Software that offers on-the-fly data monitoring through real-time reconstruction of tilt series into 3D volumes. It can automatically perform motion correction of fraction movies, fiducial-free tilt series alignment, and 3D reconstruction during tilt series recording. These reconstructed tomograms allow for impromptu data quality evaluation, identification of high- and low-quality tilt series, and exporting of selected tilt series and reconstructed tomograms for further processing, archiving, and sharing.


Tomo Live Software runs on the microscope’s Data Management Platform server, and the user interface is integrated in the Thermo Scientific CryoFlow Software portal.

Cryo-ET data workflow with Tomo Live Software

Automatic reconstruction

Autonomous estimation of all parameters needed for alignment and 3D reconstruction of tilt series acquired by Tomography Software, with the accurate transfer of metadata from Thermo Scientific cryo-TEMs, can be achieved within 5 minutes of a tilt series recording.


Tomo Live Software supports data curation by displaying quality metrics alongside the reconstructed tomograms. Define rulesets (e.g., alignment accuracy, user rating, or sample thickness estimation) that are applied during data export.


Curated tomograms can be exported in a number of formats and are ready for segmentation in Thermo Scientific Amira Software. The motion-corrected and aligned tilt series are helpful for particle picking and sub-tomogram averaging workflows.

Tomography 5 Software webinars