Morpho+ : a software package for the three-dimensional analysis of X-ray computed tomography data

Analysis software packages are a useful tool to extract quantitative information from datasets obtained with X-ray tomography. At the Centre for X-ray Tomography of the Ghent University (UGCT) (www.ugct.ugent.be) a flexible 3D analysis software package, Morpho+, has been developed. Morpho+ provides the possibility to perform 3D measurements on datasets from various research fields. The porosity or volume fraction of the volume investigated can be determined. Several segmentation algorithms are included, to subdivide the volume into different objects such as pores or grains. For these objects various parameters can be extracted, such as the surface, diameter of the maximum inscribed sphere, diameter of the minimum circumscribed sphere, equivalent diameter, mean gray value, orientation and a measure for the sphericity. Additionally, it is possible to determine the connectivity by means of the Euler Number, size of the bottlenecks and the number of neighbouring objects. A lot of effort has been made to develop new algorithms (such as a new skeletonization algorithm and a method to reduce oversegmentation) and to improve existing algorithms, to ensure that large datasets can be processed in a small amount of time. The user interface is intuitive and flexible. Every step in the analysis process is visualized to enable easy interpretation of the result

3D image analysis of a volcanic deposit

During the last decades, X-ray micro CT has become a well established technique for non-destructive testing in a wide variety of research fields. Using a series of X-ray transmission images of the sample at different projection angles, a stack of 2D cross-sections is reconstructed, resulting in a 3D volume representing the X-ray attenuation coefficients of the sample. Since the attenuation coefficient of a material depends on its density and atomic number, this volume provides valuable information about the internal structure and composition of the sample. Although much qualitative information can be derived directly from this 3D volume, researchers usually require more quantitative results to be able to provide a full characterization of the sample under investigation. This type of information needs to be retrieved using specialized image processing software. For most samples, it is imperative that this processing is performed on the 3D volume as a whole, since a sequence of 2D cross sections usually forms an inadequate approximation of the actual structure. The complete processing of a volume consists of three sequential steps. First, the volume is segmented into a set of objects. What these objects represent depends on what property of the sample needs to be analysed. The objects can be for instance concavities, dense inclusions or the matrix of the sample. When dealing with noisy data, it might be necessary to filter the data before applying the segmentation. The second step is the separation of connected objects into a set of smaller objects. This is necessary when objects appear to be connected because of the limited resolution and contrast of the scan. Separation can also be useful when the sample contains a network structure and one wants to study the individual cells of the network. The third and last step consists of the actual analysis of the various objects to derive the different parameters of interest. While some parameters require extensive calculations, others can be obtained easily. The different parameters which can be obtained are related to the size, shape and orientation of the objects. Additionally, the connectivity of a network can be analysed by comparing the set of objects before and after separation. The size of each object can be characterized by its volume, equivalent diameter and the diameter of the maximum inscribed sphere. The surface can be determined by extracting a polygonal mesh from the volume data. Calculation of Feret’s diameter reveals information about the objects elongation. Additionally, the moments of inertia can be calculated to obtain the axes of an equivalent ellipsoid. This data can be used to determine the main axis and therefore the orientation of the object within the sample. Feret’s diameter and the equivalent ellipsoid are representative for the basic shape of the object. Additionally, using a routine that fills concave regions, the convex hull of an object can be retrieved to quantify the convexity. Different ratios can be defined, which compare the surface area with the volume of the object (sphericity) or the volume of the convex hull. These ratios and the convexity characterize the objects roughness and shape. The described parameters are used to characterize volcanic deposits found in the area west of Lac Pavin (lake in Auvergne, France). The samples are taken from the most recent ‘red scoria’ layer, which is believed to be the result of the latest eruption in Western-Europe. There is however, ambiguity on the origin of the layer in terms of age and placement. The aim is to fingerprint this layer in such a way that the various eruptions in the area can be distinguished from one another. Measurements of the vesicle density, volume and connectivity of the investigated deposits provide information about the intensity of the eruption. Additionally, vesicle geometry can be related to the magmatic permeability, which is essential to the dynamics of the eruption

Latest developments in 3D analysis of geomaterials by Morpho+

At the Centre for X-ray Tomography of the Ghent University (Belgium) (www.ugct.ugent.be) besides hardware development for high-resolution X-ray CT scanners, a lot of progress is being made in the field of 3D analysis of the scanned samples. Morpho+ is a flexible 3D analysis software which provides the necessary petrophysical parameters of the scanned samples in 3D. Although Morpho+ was originally designed to provide any kind of 3D parameter, it contains some specific features especially designed for the analysis of geomaterial properties like porosity, partial porosity, pore-size distribution, grain size, grain orientation and surface determination. Additionally, the results of the 3D analysis can be visualized which enables to understand and interpret the analysis results in a straightforward way. The complementarities between high-quality X-ray CT images and flexible 3D software are opening up new gateways in the study of geomaterials

Bronnikov-aided correction for x-ray computed tomography

When a very-low-absorbing sample is scanned at an x-ray computed tomography setup with a microfocus x-ray tube and a high-resolution detector, the obtained projection images contain not only absorption contrast but also phase contrast. While images without a phase signal can be reconstructed very well, such mixed phase and absorption images give rise to severe artifacts in the reconstructed slices. A method is described that applies a correction to these mixed projections to remove the phase signal. These corrected images can then be processed using a standard filtered backprojection algorithm to obtain reconstructions with only few or no phase artifacts. This new method, which we call the Bronnikov-aided correction (BAC), can be used in a broad variety of applications and without much additional effort. It is tested on a biological and a pharmaceutical sample, and results are evaluated and discussed by comparing them with those of conventional reconstruction methods

Contributions of X-ray CT to the characterization of natural building stones and their disintegration

This paper highlights the use of the high resolution scanner at the Centre for X-ray Tomography in Ghent, Belgium (UGCT), for the 3D quantitative evaluation of the disintegration of some French natural building stones. Rocks deteriorate when they are exposed to extreme weathering factors such as a combination of water and freeze-thaw cycles or high pressure. The results of those processes can be very diverse: from element migration to crust formation to the origination of micro-cracks. Thanks to its non-destructive character, high resolution computed tomography (CT) turned out to be an excellent monitoring tool as it contributes to the characterization of the internal structure of the natural building stone. X-ray CT also provides a better insight into the micro-structural durability properties of the building stone

Advanced segmentation algorithms for the three-dimensional analysis of X-ray CT data from geomaterials

X-ray Computed Tomography (CT) is a non-destructive technique which enables the visualization of the internal structure of all kinds of samples, including geological samples. Additionally, the resulting datasets can be analyzed to obtain quantitative information. As geological samples often contain different components such as different minerals, pores and a matrix, accurate segmentation techniques are of the utmost importance in order to obtain correct results. This paper illustrates the use of advanced segmentation algorithms applied on a Belgian glauconite-rich sandstone, the Beerlegem fieldstone. These segmentation algorithms allow extraction of the different grains in the stone, setting the stage for further analysis