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Frequently asked questions

Why would I use the katana microtome?


  • If you currently do serial section TEM (ssTEM) but find that it is too time/labour intensive

  • If you currently use FIB but need to image larger volumes in a short time

  • Any biological question where you need to see the ultrastructure of a specimen

What samples can I study?

  • The most common application is for biological samples, which are generally stained and embedded in resin

  • Anything that can be cut with a diamond and show contrast in an SEM

How thin can katana microtome cut?

Short answer: Around 15nm under certain optimised conditions. For a more typical scenario with a well stained resin-embedded biological sample, you can expect to hit a lower limit of approx. 25nm. Some other materials (e.g. aluminium) can cut cleanly down to 10nm

Detailed answer: There is a complex trade-off between electron dose on the sample (and hence image quality) and cutting performance. To illustrate with some of extreme examples:

  • If you use very low electron dose (<1e/nm2) then you can cut cleanly at 10nm. However, this approach has diminishing returns since the resolution will then be limited by image noise

  • If you are taking multiple images per cut, or a very high signal-to-noise ratio (SNR) image, or using very small pixel size, then you may need to cut thicker (e.g. 100 nm) to maintain clean and uniform cutting

  • If you use a more sensitive BSE detector, you can get the same SNR from lower electron dose, so you can cut thinner

  • The SBFSEM technique usually has a sweet-spot where it is easy to operate and get good results: Accelerating voltage 2kV, 15e/nm2 (dose at sample), Modern BSE detector giving SNR >4:1 at above conditions, Pixel size 10x10x30nm

What are the optimum working conditions for katana?

This will depend on the SEM, detector, type of sample, and how you wish to balance trade-offs (e.g. do you prefer high SNR over thin cutting)

What happens if I use the incorrect operating conditions?

This won’t result in damage, but your data will be sub-optimal. Pushing the dose too high, or cutting too thin will result in failure to cut cleanly. The knife will chatter over the surface, or will take alternating thick/thin cuts. The end effect of this is a reduction in Z resolution.

Using too high an accelerating voltage will result in signal originating below the next cut. Again, this limits your actual Z resolution.

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