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An ultramicrotome that transforms a normal SEM to a volume SEM


Serial block-face SEM

In serial block-face imaging, a microtome resides inside the vacuum chamber of an SEM. A diamond knife repeatedly removes a thin surface layer from the sample block. The removed layer can be as thin as 15 nm. After each sectioning, the exposed block surface is imaged. This automated in situ method can acquire a series of electron micrographs over a large volume. 


An ultra-micro ultramicrotome

Confirmed compatible SEMs

FEI Quanta 200, FEI Quanta 250, FEI Helios NanoLab 650,

Zeiss Sigma VP, Zeiss Merlin compact, Zeiss Merlin, Zeiss Gemini 350



Hitachi SU7000

(The list is updated each time we demonstrate katana on a new SEM)

At a mere 56 mm in height, katana ultramicrotome is designed to fit inside the vacuum chamber of many SEMs. Easy installation has been at the heart of our design. The microtome can be attached to / removed from an SEM stage by a lever mechanism. All electronic signals are fed through a vacuum flange via a single connector. The user friendly design enables a quick and easy switch from your normal SEM to a volume SEM and back.

ultra is also for ultrasonic

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Think about the sawing motion you make when slicing a loaf of bread, the sample cutting force can be greatly reduced - and the surface texture of the cut improved - by oscillating the diamond knife at ultrasonic speeds. The FEA optimised knife design enables a piezo driven in-plane oscillation at an amplitude up to 170 nm at resonant frequency. The oscillation amplitude is constantly measured by a sensing piezo. The dual-piezo design allows the fine tuning of the oscillation mode which varies between different knife holders and samples.

The images on the left shows the effect of knife oscillation on 25 nm ultra-thin cutting performance of pigment granules in a squid skin chromatophore. Without knife oscillation, softer pigment granules are pulled out of the block by the knife. This behaviour is immediately prevented when oscillation is turned on.

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Nanometre precision

A precise and repeatable stepping motion in Z-direction is crucial to produce accurate Z scaling in final 3D volume data. The position of our sample stage - driven by an ultra-fast motor - is measured constantly by a nanometre resolution encoder so that any drift can be instantly corrected.


The accompanied benefits are:

1) Debris mitigation: as the knife retracts after each cut, the sample can drop hundreds of microns away from the removed material. This reduces the chance of debris falling onto the block surface by electrostatic force;

2) Reduced working distance: samples can move closer to the detector during imaging, thereby improving the collection of backscattered electrons and thus signal-to-noise ratio.

Finding cutting plane made easy

For someone who is new to ultramicrotomy, finding the cutting plane is often a daunting experience. Our carefully designed digital viewer makes this process simple and smooth. The digital viewer sits over the microtome so that the approach process can be done on an SEM stage. It has a 40 fps 2.3 MP CMOS camera coupled with a high resolution lens to create a crisp and low latency view of the knife and sample. A series of internal mirrors tracks the movement of the knife so that the blade of the diamond always stays focused and stationary on the screen.


In reality, the moving object is the knife.

Open and friendly to users

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Katana microtome is controlled via a tablet with a familiar multi-touch user interface that enables you to control the microtome with your fingertip. It communicates with our universal SEM automation software which works with existing SEM control software to conduct scanning, imaging monitoring and image saving automatically. We have always loved using open source and we believe in giving back to open source as much as we benefit from it. You can control the microtome via USB by sending serial commands which are available to users. You can build your own apps to control the microtome, whether it be a from simple cutting and actuating process, to complex automation with other instruments. 

katana microtome is now fully integrated with SBEMimage, a versatile acquisition control software for serial block-face electron microscopy developed by The Friedrich Miescher Institute for Biomedical Research. Its functions includes advanced monitoring, process control, and error handling capabilities improve reliability, speed, and quality of acquisitions. Debris detection, autofocus, real-time image inspection, and various other quality control features minimize the risk of data loss during long-term acquisitions. Adaptive tile selection allows for efficient imaging of large EM volumes of arbitrary shape. The software’s graphical user interface is optimized for remote operation. It includes a user-friendly Viewport window to visually set up acquisitions and monitor them.

To learn more about SBEMimage, please visit have a read of this article   and visit its GitHub page.


Technical specifications and accessories 


Dimension: 135 x 66 x 56 (H) mm

Z resolution: 1 nm (closed-loop)

Z travel range: 1300 μm

Diamond blade width: 1.5 mm

Knife oscillation amplitude: 0 - 170 nm

Knife oscillation frequency: 0 - 60 kHz

Minimum working distance: 3 mm (Distance from the sample to BSED)


Digital viewer - 40 fps 2.3 Megapixel CMOS USB 3.0 camera, no focusing required

Sample measurement tool - Measure sample size to estimate the total volume

Tablet PC - Multi-touch user interface (optional)

Aluminium sample pins - bag of 50

Others - 1 set of interface flange and stage adapter, aluminium carry case

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