Facilitating Soft Tissue Analysis – Unraveling Complex MicroCT Imaging Data with Amira Software

Key takeaways

• Micro-computed X-ray tomography (microCT) can be used for high-resolution, 3D visualization of a range of biological samples, including soft tissues, but transforming this data into scientific insights requires the processing of increasingly large, complex datasets.
• Thermo Scientific Amira Software is a powerful data processing tool that can simplify and accelerate complex soft-tissue analysis workflows by enabling efficient segmentation, quantitative analysis, and 3D visualization of large biological datasets.
• Researchers at the University of Oslo’s NEXT facility demonstrate this capability by turning complex soft-tissue CT scans into meaningful scientific observations.
• Amira Software combines visualization and quantitative analysis in a single platform, helping to reduce microCT workflow complexity and to increase the productivity of biological imaging research.

Too much of a good thing? The challenge of large microCT imaging datasets

Advances in computed X-ray tomography have increased the quality and resolution of microCT data, opened new avenues for the 3D investigation of biological tissues, hierarchical structures, and biomaterials. This wealth of data can be a double edged sword, however, as researchers must now find efficient ways to examine and process these large imaging datasets in order to transform them into valuable scientific information.

MicroCT soft tissue analysis at the Norwegian Centre for Nanoscale X-ray CT

At the University of Oslo, the Norwegian Centre for Nanoscale X-ray CT (NEXT) offers scientists and industrial partners access to advanced X-ray imaging capabilities and expertise. Dr. Liebert P. Nogueira is the Chief Engineer and Head of the X-ray CT Platform at NEXT; his team supports projects ranging from soft-tissue imaging and biomaterials research to dental and geological investigations. For such a multidisciplinary facility, reliable advanced image analysis is critical, which is why they leverage Thermo Scientific Amira Software in many of their workflows.

What are the challenges of soft-tissue microCT analysis?

One of the major challenges in the microCT imaging of soft-tissues is the transformation of large grayscale datasets into meaningful quantitative and biological information. Unlike highly absorbing materials such as bone or metal, soft tissues often exhibit low natural contrast; revealing their internal structures in three dimensions necessitates specialized staining protocols and higher resolution imaging, as well as advanced image-processing workflows.

Additionally, researchers often require more than just visualization of their microCT data; they need to accurately segment anatomical structures, quantify volumes, and correlate features across scales. They must also generate reproducible results from these increasingly large and complex datasets.

Advanced microCT analysis for biological imaging

To process and analyze this complex data, the team at NEXT relies heavily on Amira Software, using it not only for the reconstruction and analysis of large microCT datasets, but also for:

• Segmentation of complex biological structures
• Quantitative image analysis
• 3D rendering and anatomical reconstruction
• Preparation of publication-quality visualizations

“Amira Software has become an essential part of our workflow for soft-tissue microCT,” says Dr. Nogueira. “It allows us to efficiently process very large datasets while preserving the structural relationships that are often difficult to interpret using conventional 2D approaches.”

Combining visualization and quantitative analysis

One of the advantages of Amira Software highlighted by the NEXT team is the ability to perform visualization and quantitative analysis within a single software environment. For biological imaging projects, researchers often need to move seamlessly between visual inspection, segmentation, measurements, and data interpretation. Having these capabilities integrated into one workflow helps streamline analysis and supports collaboration across multiple disciplines. The flexibility of Amira Software also enables integration with AI-powered approaches, customized image-processing pipelines, and collaborative research workflows.

“Every project presents different analytical challenges,” explains Dr. Nogueira. “Amira Software gives us the flexibility to adapt our workflows depending on the sample type, imaging modality, and scientific question.”

Supporting remote scientific access through the EXCITE Network

In addition to supporting local research activities, NEXT also offers remote scientific services through the European EXCITE Network, a Horizon Europe infrastructure that connects advanced imaging facilities.

Using a virtual desktop environment hosted at the University of Oslo, researchers from different countries can remotely access high-performance workstations equipped with Thermo Scientific Amira and Avizo Software for advanced microCT data analysis. For many users working with large biological datasets, this remote environment makes advanced image analysis accessible without the need for specialized, local computing hardware.

“Amira Software plays a central role in our remote analysis infrastructure,” says Nogueira. “Researchers can interactively work with large 3D datasets through our VDI platform, perform segmentation and quantitative analysis remotely, and collaborate directly with imaging specialists during the analysis process.”

Turning microCT imaging data into scientific insight

As microCT imaging datasets continue to grow in size and complexity, the ability to transform this data into reliable scientific information becomes increasingly important. For the team at NEXT, Amira Software offers the necessary combination of visualization, segmentation, and quantitative analysis to support advanced biological imaging research.

“I recommend Amira Software because it provides a very powerful and flexible environment for advanced 3D image analysis,” concludes Dr. Nogueira. “For many of our projects, it is not simply a visualization tool—it is the platform that allows us to transform complex microCT data into quantitative scientific insight.”

About Dr. Liebert P. Nogueira

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