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ZEISS Volutome
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ZEISS Volutome In-Chamber Ultramicrotome for Serial Block-Face SEM

Image the ultrastructure of biological, resin-embedded samples in 3D over large areas. ZEISS Volutome is an end-to-end solution from hardware to software including image processing, segmentation, and visualization. The ultramicrotome can be easily replaced by a conventional SEM stage, converting your 3D FE-SEM into a standard, multipurpose FE-SEM, making your system adaptable to a multi-purpose environment.

  • Automated cutting, image acquisition, and pre-processing
  • Superb 3D imaging of biological samples
  • A complete ZEISS solution from hardware to software

Volume Data Acquisition through Automated Sectioning and Imaging

See ZEISS Volutome in Action

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Save Time with Automated Cutting, Image Acquisition, and Pre-processing

Serial block-face imaging requires stable acquisition conditions over a long period of time. ZEISS Volutome allows highly automated and unattended cutting and imaging. The cutting cycle is sped up and image acquisition is accelerated using the dedicated detector ZEISS Volume BSD. During image acquisition, images are simultaneously pre-calculated for stitching and z-stack alignment – meaning results are at your fingertips in one click.

Mouse brain tissue acquired with ZEISS Volutome and ZEISS GeminiSEM; pixel size: 3 nm. Sample courtesy of Christel Genoud, Université de Lausanne, Switzerland

Superb 3D Imaging of Your Biological Samples

Resin-embedded samples are challenging to image. High quality images with good contrast are normally acquired with higher acceleration voltages – which can damage your sensitive sample. Imaging at low kV ensures sample integrity – but produces images with less contrast. ZEISS Volume BSD is the new high-speed, high-sensitivity detector specially designed for ZEISS Volutome, ensuring high-contrast images even at low kV. In combination with Focal Charge Compensation, charge-prone samples can be easily imaged by charge neutralization at the block face.

Caption: Mouse brain tissue acquired with ZEISS Volutome and ZEISS GeminiSEM; pixel size: 3 nm. Sample courtesy of Christel Genoud, Université de Lausanne, Switzerland

3D reconstruction of mouse brain neurons. Sample courtesy of Christel Genoud, Université de Lausanne, Switzerland

One Solution – One Contact

ZEISS Your Trusted Partner for Volume EM

Providing the complete, integrated serial block-face solution from hardware to software, ZEISS Volutome is ideal for users with a vested interest in streamlining their number of equipment suppliers. Whether you have questions about the ultramicrotome, the detector or FE-SEM, or even the applications, rest-assured ZEISS is your contact.

Caption: 3D reconstruction of mouse brain neurons. Sample courtesy of Christel Genoud, Université de Lausanne, Switzerland

The Hardware Behind ZEISS Volutome

The hardware components of ZEISS Volutome work hand in hand to facilitate the streamlined workflow, from sample alignment and knife approach to image acquisition.
  • Image of Volutome open chamber

    In-Chamber Ultramicrotome

    With Volutome, you can easily transform your ZEISS Sigma or ZEISS GeminiSEM to a serial block-face imaging system.

  • ZEISS Volutome accessories: Stemi 305 sample adjustment stand and holder

    Alignment Stand and Sample Holder

    Before mounting the sample inside the ultramicrotome, the sample is inserted into a specially designed sample holder and centered by means of a ZEISS stereo microscope.  

  • ZEISS Volutome product photo: Illumination for sample to knife adjustment

    Light Sources

    Once the sample is placed in the ultramicrotome, light sources make the reflection of the knife on the sample surface clearly visible and show you when the knife is close to the sample.

  • Image of ZEISS Volutome controller

    ZEISS Controller

    Using the ZEISS Controller, the sample can be precisely moved towards the knife, monitored either through the binoculars of a stereo microscope or digitally on a screen.

  • Image of ZEISS Volume BSD

    BSE Detector

    ZEISS Volume BSD is your optimized detector for serial block-face imaging – specifically enhanced for the imaging with low acceleration voltages and fast scanning speeds.  

ZEISS Focal Charge Compensation

Elimination of Charging Effects
Arabidopsis thaliana imaged without Focal CC (left) and with Focal CC (right). Without Focal CC, the image is deteriorated by charging effects. Sample courtesy of Prof. S.C. Zeeman, ETH Zurich, Switzerland.
Arabidopsis thaliana imaged without Focal CC (left) and with Focal CC (right). Without Focal CC, the image is deteriorated by charging effects. Sample courtesy of Prof. S.C. Zeeman, ETH Zurich, Switzerland.
Arabidopsis thaliana imaged without Focal CC (left) and with Focal CC (right). Without Focal CC, the image is deteriorated by charging effects. Sample courtesy of Prof. S.C. Zeeman, ETH Zurich, Switzerland.

High-Quality Imaging of Resin-Embedded Biological Samples

Specimen charging, particularly in samples containing large regions of bare resin, results in a significant degradation in image quality and distortion. Typically, charging is mitigated by applying variable pressure, however this is at the expense of signal-to-noise ratio and resolution.

ZEISS Focal Charge Compensation eliminates specimen charging. A gas injection system is precisely located above the sample. Nitrogen is guided directly onto the block-face surface while the chamber is maintained under high vacuum. This eliminates charging and assures high image quality. The needle retracts automatically during the cutting cycle, so the workflow is uninterrupted and high acquisition rates are maintained.

Illustration of ZEISS Focal Charge Compensation - 1

1

Electrons of the primary electron beam interact with the specimen creating charging effects. Secondary electrons are released from the specimen and generate negative charging on the surface. The detector will be overwhelmed by electrons.

Illustration of ZEISS Focal Charge Compensation - 2

2

Through the Focal CC needle, nitrogen gas is applied to the sample and forms a local gas cloud above the specimen surface. Primary and backscattered electrons from the specimen surface ionize the nitrogen molecules.

Illustration of ZEISS Focal Charge Compensation - 3

3

The positively charged nitrogen molecules neutralize the specimen surface. Thus, charging effects are minimized.

Illustration shows the principle of tiling and stitching for large area imaging.
Illustration shows the principle of tiling and stitching for large area imaging.

Illustration shows the principle of tiling and stitching for large area imaging.

Illustration shows the principle of tiling and stitching for large area imaging.

Large Volume Imaging

Reveal the Ultrastructure of Your Sample in a Wider Context

ZEISS Volutome offers a robust stage solution. The ultramicrotome stage reduces drifting effects and makes large volume imaging over a long period of time possible. You can access these large volumes by acquiring single 2D images at up to 32k × 32k pixel resolution.

For applications that require you to push the boundaries of single 2D imaging, you can stitch multiple single images together to create one larger mosaic image. Mosaic imaging is of special interest when cells or cellular structures need to be traced across a wide range in x, y and z. A prominent example is Connectomics: the neuronal network and connections between nerves must be investigated comprehensively over wide, continuous volumes.  

From Image Acquisition to 3D Results
From Image Acquisition to 3D Results

From Image Acquisition to 3D Results

ZEISS Software for Serial Block-Face Imaging

ZEISS software combines the individual Volutome hardware components to make the serial block-face workflow smooth and easy-to-use. The cutting operation as well as the imaging process are controlled by ZEISS ZEN core. ZEN core workbenches provide intuitive structure to control setup, sample to knife approach and parameters for cutting and image acquisition.

Once the data is collected and the pre-calculation is applied for stitching and z-stack alignment, the results can be visualized and processed with ZEISS arivis Pro.

Take your results a step further, with software from the ZEISS arivis product family you can an-notate, segment, and analyze your data – getting the most information out of your images.  

ZEISS Volutome at Work

Serial Block-Face SEM Application Examples

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Mouse brain tissue processed, segmented, and visualized with ZEISS arivis (red: blood vessel, cyan: nuclei, blue: neurons). Sample courtesy of Christel Genoud, Université de Lausanne, Switzerland

Neuroscience

Neuroscientists continue to pursue better understanding of neuronal connections and signaling pathways. Serial block-face imaging is the appropriate solution to image and follow neurons with long and thin protrusions, such as dendrites and axons. ZEISS Volutome enables acquisition of large mosaic images over all three dimensions at high resolution. Sections as thin as 25 nm with pixel sizes as small as 3 nm can be cut to follow the dendrites and axons precisely over long distances.

3D reconstruction of mouse brain tissue

  • Pixel size: 6 nm
  • Cutting thickness: 25 nm
  • Dimensions: 43 µm × 43 µm × 45 µm (1800 sections)
  • EHT: 1.2 kV / Ip: 90 pA
  • Dwell time: 0.8 and 1.6 µs, respectively
  • Acquired with ZEISS GeminiSEM 460
Genetically modified stem cells cut and imaged with ZEISS Volutome in a ZEISS GeminiSEM 460 to investigate morphological changes. Various cellular components, such as mitochondria or nuclei can be easily identified and analyzed. Cellular components were annotated, segmented, and visualized with ZEISS arivis.
Genetically modified stem cells cut and imaged with ZEISS Volutome in a ZEISS GeminiSEM 460 to investigate morphological changes. Various cellular components, such as mitochondria or nuclei can be easily identified and analyzed. Cellular components were annotated, segmented, and visualized with ZEISS arivis.

Sample courtesy of Alexandra Graff-Meyer and Marc Buehler, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland

Sample courtesy of Alexandra Graff-Meyer and Marc Buehler, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland

Cell Biology

High resolution imaging is necessary to visualize the ultrastructure of cells and cellular components. Samples with large areas of bare resin are particularly prone to charging. Focal Charge Compensation avoids the charging effects and delivers high-quality images. The sensitivity of ZEISS Volume BSD permits low kV imaging without sacrificing image contrast or acquisition time. Under these conditions, various cellular components, such as mitochondria, Golgi, and even vesicles can be identified and analyzed.

Genetically modified stem cells

  • Pixel size: 10 nm
  • Cutting thickness: 30 nm
  • Dimensions: 51 µm × 51 µm x 15 µm (~550 sections)
  • EHT: 1.5 kV / Ip: 100 pA
  • Dwell time: 2.8 µs
  • Acquired with ZEISS GeminiSEM 460

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Arabidopsis thaliana leaf prepared according to the protocol developed by NCMIR. Sample Courtesy of Prof S. C. Zeeman, ETH Zürich, Switzerland

Plant Science

Plant science is about understanding the microscopic relationships that are impacted by drought, climate change, pollution, and genetic factors. These translate into health and disease states in plants which impact crop yield, food production and, ultimately, human wellbeing. Imaging plant samples can be challenging due to their anatomy, such as cell walls and vacuoles. For serial block-face imaging, biological samples must be embedded in resin. Low kV, high-speed acquisition with Volume BSD, and the use of Focal Charge Compensation enable high-contrast plant imaging without compromise.

Arabidopsis thaliana leaf

  • Pixel size: 6 nm
  • Cutting thickness: 40 nm
  • Dimensions: 36 µm × 36 µm × 16 µm (400 sections)
  • EHT: 1.5 kV / Ip: 110 pA
  • Dwell time: 1 µs
  • Acquired with ZEISS GeminiSEM 460
3D ultrastructure of a mouse skeletal muscle prepared according to the Hua sample preparation protocol (Hua et al., 2015, Nat. Comm). Sample courtesy of the Experimental Neurology Unit, University of Milano-Bicocca, Monza, Italy
3D ultrastructure of a mouse skeletal muscle prepared according to the Hua sample preparation protocol (Hua et al., 2015, Nat. Comm). Sample courtesy of the Experimental Neurology Unit, University of Milano-Bicocca, Monza, Italy
3D ultrastructure of a mouse skeletal muscle prepared according to the Hua sample preparation protocol (Hua et al., 2015, Nat. Comm). Sample courtesy of the Experimental Neurology Unit, University of Milano-Bicocca, Monza, Italy

Tissue Imaging

Volume electron microscopy enables imaging of much larger sample sizes, making visualization of larger tissue sections a more routine application for life scientists across many disciplines. Whether you work with tumors and biopsies, organ or tissue sections, organoids, embryos of model organisms and more, serial block-face imaging allows large sample volumes to be imaged and analyzed within a broader 3D context. Investigate your samples in healthy or diseased states, or examine the effects of metabolic changes, genetic factors, drug treatments, and more.

Mouse skeletal muscle

  • Pixel size: 3 nm
  • Cutting thickness: 100 nm
  • Dimensions: 18 μm × 15 μm × 25 μm (250 sections)
  • EHT: 2 kV / Aperture: 20 μm, high current
  • Dwell time: 1 µs
  • Acquired with ZEISS GeminiSEM 360

Related Applications

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    ZEISS Volutome

    Volume Data Acquisition through Automated Sectioning and Imaging
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