How to Select Complex Regions of Interest in Micro-CT

In micro-CT 3D X-ray imaging, regions of interest are not always simple or regular. Often you need to select more complex regions. These ROIs can be selected automatically using two powerful plug-ins from Bruker:

  • ROI shrink-wrap
  • Primitive ROI

Blue Scientific is the official distributor for Bruker Micro-CT in the UK and Nordic region. For more information or quotes, please get in touch.

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Selecting Regions of Interest

Bruker’s ROI shrink-wrap and primitive ROI plug-ins are extremely useful tools for defining the region of interest automatically. They are particularly powerful in these cases:

  • Samples with complex geometry – where it would be difficult or impossible to define the region of interest manually.
  • Studying points where objects touch the outside of the volume of interest.
  • Analysing large numbers of samples consistently.

ROI Shrink-Wrap

With the ROI shrink-wrap plug-in, you can generate regions of interest automatically by adapting to the shape of selected objects. There are three modes:

  1. Shrink-wrap
  2. Fill-out
  3. Adaptive

There are additional options for stretching over holes, removing pores and trimming lumps – particularly useful for uneven and irregularly-shaped samples.

A method note (MN121) is available with a full description of these options, together with practical examples can be found in ‘MN121 – ROI shrink-wrap’. This is available for current users on the Bruker Micro-CT sharing portal. If you’d like a copy please get in touch.

Bruker Shrink-Wrap Micro-CT Plug-in

With the ROI shrink-wrap plug-in you can automatically select regions of interest around complex shapes.

Primitive ROI

With the primitive ROI plug-in, you can create an image of the region of interest exclusively containing a certain edge as the binary object. You can also select the intersection (infimum) or addition (supremum) of that image together with a pre-existing ROI.

This is useful when selecting or excluding structures that are touching particular edges of the image cube – particularly when used together with the ROI shrink-wrap plug-in (fill-out).

This technique is described in more detail in method note MN120, available for users on Bruker’s sharing portal (contact us if you’d like a copy). The method note includes a useful example from the field of geology: quantifying fluid percolation properties inside rock cores, when you need to analyse the vertically-connected pore space. With the plug-in, this region can easily be selected automatically.

Micro-CT Scan of Sandstone

Volume rendering of Vosges sandstone. Connected pore space from top to bottom was selected using the primitive ROI and ROI shrink-wrap plug-ins. Colour-coded by local thickness. Scanned with the Bruker Sky Scan 2214 nano-CT (1.10 μm image pixel size).

Further Information

Blue Scientific is the official distributor of Bruker Micro-CT in the UK and Nordic region. If you’d like any more information, demonstrations or quotes, please contact us:

 Contact us on +44 (0)1223 422 269 or

Bruker micro-CT systems

More posts about micro-CT