For background information on soft x-ray tomography, please download our Primer.

Below, you can find links to tutorials covering all aspects of the imaging carried out at the NCXT. If you notice an error, or have suggestions how to improve the clarity or increase the scope of these tutorials, please contact us.

We are also building a library of in-depth instructional videos covering all aspects of soft x-ray tomography, from making capillaries and preparing specimens to setting up the microscope and collecting data.

Preparing Specimen Mounting Capillaries

Pulling & Glueing Capillaries - Instructions on how to make capillaries for mounting your specimens

Aliquoting Gold Nanoparticles - Key to consistent, isolated fiducial markers

Dipping & Clipping Capillaries - How to coat capillaries with gold nanoparticles

Specimen Preparation and Mounting

Cryo-Transferring specimen to the soft x-ray microscope.

Data Processing and Tomographic Reconstruction

IMOD - Alignment of projection series and reconstruction by Filtered Back Projection.

ASPIRE - Iterative reconstruction method

Arec3d - Automatic alignment / iterative reconstruction method


We primarily use - and recommend - the software package Amira for segmenting tomographic reconstructions. Currently, we support the use of two versions of Amira, 6.0 and 5.3.3.

Amira 6.0

- Cropping the reconstruction in Amira 6.0

Amira 5.3

Cropping the reconstruction in Amira 5.3

Tips on cropping out the capillary, buffer, and other cells from the reconstructed field of view

Resolution and Radiation Damage

* Tutorial/Background on Radiation damage. Coming soon