Thermo Fisher Scientific Amira/Avizo are powerful, multidisciplinary tools for 3D visualization and analysis designed for the exploration, reconstruction, and quantitative analysis of complex scientific and industrial data.

These platforms are widely used in various research and engineering fields, including materials science, life sciences, earth sciences, engineering, and industrial inspection. Both Amira and Avizo belong to the same software family and have the same core architecture, but are designed for different domains: Amira primarily serves life sciences and biomedical research, while Avizo focuses on materials science, engineering, and industrial applications.

1. Main capabilities

Both Amira and Avizo software are designed to manage 3D and 4D datasets obtained from imaging methods such as:

• Micro X-ray computed tomography (micro CT)
• Scanning electron microscope (SEM)
• Focused Ion Beam (FIB-SEM)
• Magnetic resonance imaging (MRI)
• Confocal microscope
• Synchrotron tomography and neutron tomography

They enable users to import, visualize, segment, analyze, and present their data in a unified environment.

2. Data visualization

Amira and Avizo offer advanced 3D rendering techniques for:

• Volumetric Rendering: Enables realistic visualization of volumetric data using direct volumetric rendering and transfer functions to highlight specific structures.
• Surface Rendering: Generates polygonal surfaces from segmented regions, allowing for 3D surface inspection and output to CAD or 3D printing formats.
• Slice and Orthogonal Views: Allows users to explore data sets slice-by-slice across different pages.
• Animation and keyframe tools: Facilitate dynamic presentation and time-dependent visualization (4D datasets).
• These visualization features help researchers intuitively understand structural relationships, morphology, and dynamics in their datasets.

3. Image segmentation and processing

Segmentation is at the heart of quantitative 3D analysis. Amira and Aviso include a comprehensive suite of automated, semi-automated, and manual segmentation tools, such as:

• Threshold setting and area growth
• Watershed segmentation
• Machine learning-based segmentation (using tools like interactive learning)
• Morphological filtering and noise removal
• Tagging fields to manage multiple areas

Users can segment biological tissues, material phases, or geological structures with high accuracy and reproducibility. Segmentation workflows can be customized and automated using scripts and pipelines.

4. Quantitative analysis and measurement

After segmentation, the software can calculate precise measurements and statistics, including:

• Geometric properties: volume, surface area, shape descriptors, and center of mass
• Porosity and Density Analysis: Common in Materials and Geological Studies
• Grain or cell statistics: size distribution, orientation, and connectivity
• Pore ​​network modeling: Extracting pore bottleneck networks and simulating fluid flow
• Skeletalization and network analysis: for vascular systems, neural networks or fibrous materials
• Mechanical and structural simulation: Using integrated finite element analysis (FEA) modules to predict the mechanical behavior of structures derived from 3D data

These features make Amira and Avizo not only visualization tools, but also complete 3D data analysis environments.

5. Automation and customization

To manage large data sets and repetitive workflows, both platforms support:

• Scripting and automation: via Python scripting interface
• Batch processing: for repetitive operations on multiple data sets
• Custom Module Creation: Users can design custom workflows or analytics modules using the platform’s development framework.
• This flexibility allows researchers and engineers to tailor the software to their specific needs and integrate it with other analysis pipelines.

6. Applications by domain

Amira – Life Sciences

• Neuroscience: Visualization and tracking of neural structures, brain mapping, and connectivity analysis
• Cell biology: 3D reconstruction of cells, organelles, and tissues from light or electron microscope data
• Developmental biology: tracking morphological changes in time-lapse datasets (4D)
• Medical imaging: Analysis of MRI, CT or confocal data for anatomical modeling and research
• Avizo – Materials Science and Engineering
• Metallurgy: Grain structure analysis, inclusion detection and texture quantification
• Composites and polymers: fiber orientation analysis, volume fraction, and stress simulation
• Additive Manufacturing: Defect Inspection, Porosity Analysis, and Dimensional Validation of 3D Printed Parts
• Earth Sciences: Studies of rock porosity and permeability, mineral phase distribution, and structural geological modeling
• Semiconductors and electronics: microstructure inspection, hole and crack detection, and layer analysis

7. User interface and workflow

Both platforms feature an intuitive, module-based interface where users can visually build workflows by connecting modules that represent operations such as filtering, thresholding, or visualization. This node-based system makes it easy to:

• Designing repeatable workflows
• Dynamic modification of analysis steps
• Visualizing the data processing pipeline clearly

The user interface integrates 2D and 3D displays, parameter panels, and real-time previews to support interactive exploration.

8. Merge and output

Amira and Avizo support interoperability with a wide range of file formats, including:

• Image data: TIFF, PNG, DICOM, RAW, HDF5
• 3D meshes: STL, OBJ, PLY
• Simulation data: CSV, VTK or finite element meshes

They also allow the output of results and visualizations as high-quality images, animations, and videos for scientific publications or presentations. Integration with other software (e.g. MATLAB, COMSOL, ANSYS) further extends their analytical power.

9. Performance and Scalability

To handle large, high-resolution datasets, Amira and Avizo use optimized memory management and GPU acceleration. They are designed for efficient performance on high-end workstations and support:

• Multi-core CPU processing
• GPU-based volume rendering
• Parallel computing for batch tasks

This enables interactive exploration of datasets ranging from microscopic cellular structures to macroscopic industrial components.

Thermo Fisher Scientific Amira/Avizo are industry-leading solutions for 3D and 4D data visualization and quantitative analysis. Combining powerful image processing, segmentation, and simulation tools with high-quality visualization and automation capabilities, these platforms enable researchers and engineers to gain deeper insight into the structure and behavior of complex materials and biological systems. Whether for advanced life science research or precision materials engineering, Amira and Avizo bridge the gap between imaging and quantitative understanding, transforming data into scientific discovery.