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Cryo electron tomography (cryoET) is a groundbreaking technology for 3D visualization and analysis of biomolecules in the context of cellular structures. The use of this technology enables a better understanding of the structural basis of cellular processes, which is essential for understanding cell functions. Unlike other biological imaging techniques, cryoET is a label-free cryogenic imaging technique that does not require chemical fixation or staining. Instead, cells are preserved in their native state by flash freezing (vitrification). In this way, structural information about organelles and individual proteins is linked with their exact spatial arrangement within the cell. This unique capability holds enormous potential for cell biology, making cryo electron tomography a highly promising technology.

Electron Microscopy

Cryo Electron Tomography Workflow

Intracellular structure analysis with cryo electron microscopy.


Cryo-Tomography workflow


Step 1: Sample preparation by vitrification

Cells prepared by routine culture methods are grown on carbon-coated gold electron microscopy (EM) grids. In order to preserve the native cellular environment, cells are not stained but flash-frozen directly on the EM grid. The cryogenic freezing process is so fast that liquid water forms non-crystalline vitreous ice, thus avoiding the damage caused by the formation of crystals at slower freezing rates. This process preserves the ultrastructure of the flash-frozen cell. Sample freezing is performed in a semi-automated manner using a Thermo Scientific Vitrobot System.


Step 2: Localization by fluorescence

Locating the structure of interest can be difficult in the vast complexity of the natural cellular environment. However, using cryo-correlative microscopy, the structures of interest are identified in the cryo-fluorescence light microscope, the Leica Cryo CLEM system. A dedicated cryo stage keeps the sample in its vitrified state during cryo-fluorescence imaging. The vitrified sample, along with the coordinates of the target regions for milling, is transferred to the Thermo Scientific Aquilos Cryo-FIB (cryo-focused ion beam electron microscope) in a dedicated cartridge system that safeguards the sample from contamination. Within the Aquilos Cryo-FIB, the new optional Thermo Scientific iFLM Correlative System combines light and electron microscopy into one system, eliminating extra sample transfer steps and enabling users to create a streamlined cryo-correlative solution for cryo-tomography. The iFLM (Integrated Fluorescence Light Microscope) Correlative System delivers the localization of fluorescent targets inside the chamber, allowing users to check the fluorescence signal inside milled lamellae and correlate two imaging modalities directly within one system.


Step 3: Thinning by milling

After preselection and targeting in the Leica Cryo CLEM system, the sample is transferred to the Thermo Scientific Aquilos Cryo-FIB, a dedicated Cryo-DualBeam electron microscope for thinning. The Aquilos Cryo-FIB combines a scanning electron beam (SEM) and a focused ion beam (FIB). The electron beam is used for imaging the sample, and the ion beam ensures precise removal of material from vitrified cells. Following localization by correlative microscopy, the focused ion beam is used to prepare a thin, electron-transparent lamella by removing material above and below the target region. The cryo-lamella contains the region of interest and can be milled as thin as 100–200 nanometers. There is no mechanical sectioning with the Aquilos Cryo-FIB. Instead, the vitrified sample is thinned with the help of a focused beam of gallium ions that is scanned across the frozen sample surface, removing surface atoms in a layer-by-layer fashion in a process called sputtering (also referred to as ion beam milling). Sample thinning is essential for the tomography workflow because the electron beam in the TEM can only pass through samples that are thin enough to transmit 200–300 keV electrons. Cryo-FIB thinning is a straightforward and more manageable method compared to cryo-ultramicrotomy, and it avoids intrinsic cutting artifacts of mechanical sectioning under cryo-temperatures (e.g. compression in the cutting direction).


Step 4: Electron cryo-tomography

After the milling step, thin cryo-lamellas are transferred to the Thermo Scientific Krios Cryo-TEM (cryo-transmission electron microscope), where the actual tomographic image acquisition takes place. The images in the tomographic series are acquired by tilting the sample in known increments. Individual projection images are then computationally combined in a procedure known as back-projection, which creates the 3D tomographic volume.

CryoET visualization and structural analysis

Step 5: Visualization and structural analysis

The 3D tomogram that features cellular structures can be segmented and colored in a variety of ways to enhance its display and presentation by using Thermo Scientific Amira Software, a universal 2D-5D platform for advanced visualization and analysis. From the tomogram, small subsets of data that contain the structures of interest can be computationally extracted and subjected to image-processing methods. Image processing allows researchers to achieve a resolution in the nanometer range while maintaining the best possible structure preservation.


Cryo Electron Tomography - How it works

Tomography 5 Software

Preparation of cells for cryo-electron tomography

Cryo Electron Tomography - How it works

Tomography 5 Software

Preparation of cells for cryo-electron tomography


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Thermo Scientific Krios G4 Cryo transmission electron microscope (TEM)

Krios G4 Cryo-TEM

  • Improved ergonomics
  • Fits more easily into new and existing labs
  • Maximized productivity and automation
  • Best image quality for high-resolution 3D reconstruction
Thermo Scientific Aquilos 2 cryo focused ion beam (FIB)

Aquilos 2 Cryo-FIB

  • Automation enables production of multiple lamellas
  • Target and extract your structure of interest with lift-out nano-manipulator
  • 3D visualization for high-resolution tomography
Thermo Scientific Vitrobot vitrification sample system

Vitrobot System

  • Fully automated sample vitrification
  • Blotting device
  • Semi-automated grid transfer
  • High sample throughput
Thermo Scientific Amira 2D-5D visualization Software

Amira Software
Life Sciences

  • Explore 2D-5D bioimaging data
  • Identify and understand structures
  • Obtain statistical information
  • Share reports and stunning animations
Thermo Scientific Auto Slice and View 4.0 serial section electron microscopy software

Auto Slice and View 4.0 Software

  • Automated serial sectioning for DualBeam
  • Multi-modal data acquisition (SEM, EDS, EBSD)
  • On-the-fly editing capabilities
  • Edge based cut placement
Thermo Scientific Maps electron microscopy software

Maps Software

  • Acquire high-resolution images over large areas
  • Easily find regions of interest
  • Automate image acquisition process
  • Correlate data from different sources
Thermo Scientific TEM Tomography 5 software

Tomography 5

  • Automated multi-site batch tomography
  • Automatic cassette mapping
  • Dose symmetric tilt scheme for optimal electron dose
  • Fully integrated with Selectris Imaging Filters
Thermo Scientific Falcon 4i Electron Detector

Falcon 4i Detector

  • High throughput for more images per hour
  • Unsurpassed imaging quality with high DQE
  • Lossless data compression with EER

EM Services for Cryo-Electron Tomography

  • Quickly achieve data through workflow validation and training
  • Maximize outcomes with committed system uptime and monitoring
  • Committed support from team of service experts

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