New software tool visualizes the inside of 3D images
A new open-source software tool helps see the inside of 3D and 4D images, providing insight into embryonic mouse heart development.
3D and 4D imaging, which is 3D imaging combined with time to show movement, are fast becoming standard in the life sciences. However, visualizing inside the volume can be challenging. Now, researchers Shang Wang and Andre Faubert from Stevens Institute of Technology (NJ, USA) have developed a tool that can visualize the inside of 3D and 4D images, allowing them to investigate the dynamics of embryonic mouse heart development.
When using 4D optical coherence tomography (OCT) to study the cardiac looping stage of embryonic mouse heart development, the researchers encountered a challenge. The looping stage is a vital stage of heart development; however, little is known about it because the convoluted shape of the heart tube makes it difficult to visualize and analyze.
To tackle this issue, the researchers developed an open-source, real-time software tool called clipping spline. The tool removes certain voxels (3D pixels) to reveal the structure of interest inside a 3D or 4D image. The process, called volume clipping, is similar to cutting a solid object with a knife to view what’s inside.
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The most common method for volume clipping involves clipping planes, which function like a straight knife cut. However, the simplicity of their geometry prevents the formation of concave surfaces, which limits their ability to display complex structures.
To overcome this, the researchers applied the thin plate spline (TPS) to volume clipping for the first time. The TPS is a type of smooth, 3D surface defined by a set of control points in the way that it intersects all the control points with minimal curvature. As the surface is adjustable, users can move, control or delete control points to refine its shape and position, allowing it to be adapted to complex structures. Since the TPS is defined using mathematical parameters, it is possible to carry out algorithmic transitions, like moving, splitting or merging control points, which enables smooth 4D volume clipping and dynamic visualizations.
The researchers applied the clipping spline to OCT data of embryonic mouse heart development, tracking myocardial dynamics over 12.8 hours of development across 712 time points. The tool allowed them to visualize multiple parts of the convoluted heart tube simultaneously, providing a more comprehensive view of the dynamics.
“It is simply amazing to see these developmental processes taking place, and it inspires new thoughts and hypotheses that could lead to significant insights into how the mammalian heart develops,” commented corresponding author Wang. “Studying and understanding biological development is not only essential for improving the clinical management of congenital diseases but is also foundational for many other biomedical areas, such as cancer and regenerative medicine.”
While the researchers used the clipping spline with 4D OCT data, the tool can be used for volumetric images from any imaging technique. They’re now looking at developing other advanced image processing methods using the clipping spline and applying the clipping spline to investigate embryonic heart development further.
