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University of Glasgow uses Amira software to analyze vascular structures

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By Dr. Craig J Daly, School of Life Sciences, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow G12 8QQ. Scotland.

The School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow performs advanced studies on cardiovascular system, and provides degree programmes and courses in Life Sciences, that are built upon this extensive research activity, utilizing innovative research and teaching practices.

The vascular wall: a complex and fascinating structure

The vascular (arterial or venous) wall is a fascinating structure. At the simplest level, we can think of the wall as being composed of three distinct, but interacting, layers (adventitia, media & intima; Figure 1). The vascular wall changes its structure in conditions such as hypertension which can cause a thickening of the wall. Unfortunately, the details of this 'remodeling' process are poorly understood.

Therefore, studying the 3D architecture may provide vital clues for future therapeutic targets.


Amira 3D software: visualize to understand

Researcher at the University of Glasgow have been using Amira software since version 2.3 following a demonstration of the software at an event hosted by Silicon Graphics in the Glasgow Science Center. It was clear that the system offered significant advantages over other available software at the time. To this day, Amira software continues to offer unique functionality that is essential to the work-flow in the College of Medical, Veterinary & Life Sciences.

Figure 1: Confocal Microscopy, 3D scan of a mesenteric artery wall. The top panels show the original data in 'voltex' format. The lower panels show the result of segmentation and labeling. In this 'IsoSurface' format the different colored structures are represented as a wireframe mesh which can be exported to other software packages. The left-hand panels show the outer 'adventitial' surface. The right-hand panels show the inner 'intimal' surface and its endothelial cells.
Figure 2. Nerves (yellow) on the surface of the blood vessel extend out into the (round blue) fat cells known as 'perivascular adipocytes' or 'perivascular adipose tissue' (PVAT). The physiological role of the nerve-PVAT interaction is poorly understood.

Studying perivascular tissue innervation

Recently attention has been focused on the perivascular adipose tissue (PVAT, Figure 2) that surrounds most blood vessels. Of particular interest is the way in which nerves on the surface of the blood vessel could potentially influence the function of the PVAT (Bulloch & Daly, 2014).

We are currently using Amira to analyze the degree of PVAT innervation in different types of blood vessel and in different clinical conditions (i.e. hypertension, diabetes, obesity).

A novel approach for physiology teaching

In addition to studying the vascular wall as a research topic in cardiovascular science, there is also a requirement to teach students about the biology of the vascular wall. We have used 3D animations in an attempt to enhance student learning through the use of sophisticated animation packages such as Autodesk Maya and 3DsMax (Daly et al., 2014). Amira software has become a vital component of the data workflow. Our aim is to maintain anatomical accuracy in any of the movie scenes that we build. Therefore, flexible segmentation tools and accurate mesh generation are crucial. Unlike most animation packages, Amira software works very well with surfaces containing high polygon counts. Therefore, prior to exporting a mesh, the ability to reduce the number of polygons whilst retaining a high degree of detail is extremely important.

Figure 3. Mesh Reduction. The surface shown in yellow (PVAT) was generated by Amira using 1.8 million faces (left). This was simplified to 500,000 faces (middle) without significantly altering the surface detail (right). The surface would be simplified further until loss of detail becomes an issue. The resulting mesh can then be exported to other software for sculpting and animation.

Images and text are courtesy of University of Glasgow

1. Daly CJ, Clunie L & Ma M (2014) From Microscope to Movies; 3D animations for teaching physiology. Microscopy and Analysis, I (September) 7-10.

2. Bulloch JM & Daly CJ (2014). Autonomic nerves and perivascular fat: interactive mechanisms Pharmacology & Therapeutic ;143(1):61-73