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Electron Microscopy Solutions

Amira-Avizo Meshing for FEA/CFD

3D tetrahedral mesh generation for advanced simulation

Computer Aided Engineering (CAE) is used in many fields, such as automotive, aerospace and biomechanics. Expensive experiments are being replaced by numerical simulations, allowing faster time to market while reducing costs. Simulations also help to advance understanding in many research themes. CAE areas include stress analysis using Finite Element Analysis (FEA) or thermal and fluid flow analysis using Computational Fluid Dynamics (CFD). Those analyses are combined with imaging techniques such as microCT to better understand and predict properties and to aid in creation of geometries for finite element models (simulation inputs).

Thermo Scientific™ Amira and Avizo Software provide a fast and robust meshing engine to automatically create simulation inputs from 3D labeled images. Amira and Avizo Software generate high-quality mesh with smoothed conforming interfaces from large multi-material segmented images. The user has fine control over size element distribution, while Amira and Avizo Software preserve thin structures and topology. Meshes can be exported to major solver’s format along with boundary conditions. Amira and Avizo Software also provide import of the solver’s outputs for post-processing the results with advanced visualization tools.

Application examples:

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Courtesy of National Laboratory Animal Center - National Applied Research Laboratories, Taiwan

Bone strength analysis in osteoporosis research

Assessing bone strength through finite element simulation is a well-established method for better understanding the mechanisms and prognosis during the course of osteoporosis. With advancements in image acquisition technologies to acquire structural bone data at higher resolution levels, the demands on the post-processing and 3D geometric reconstruction workflow become increasingly higher. 

The segmentation tools supplied with Amira Software allow for the design of workflows for the automatic separation of cortical vs. trabecular bone. These separated tissue types can then be meshed with differently sized finite elements in order to simulate the fine tension and compression lines through the trabecular bone, while efficiently simulating coarser tensions in the cortical bone, completing one of the most flexible and performant image-to-simulation workflows on the market. 

Upper airway flow analysis in corrective rhinosurgery research

Understanding the passage of air through the upper airways is crucial for planning corrective rhinosurgery when undisturbed airflow is inhibited by persistent obstructions or deformities. To better understand the required extend of corrective actions, airflow through the upper airways must be analyzed on an individual basis. For this, anatomical images are used in this study to perform geometrical 3D reconstruction of the upper airways.

The novel meshing functionality in Amira Software is able to produce high-quality volume meshes that are ready to be used in any third-party computational fluid dynamics software. The fine quality control that this new functionality offers enables researchers to improve mesh quality where it matters, while ensuring efficient simulation through coarser meshes in areas that are not as relevant. All this is integrated with unprecedented performance. The simulated CFD data can then be imported into the Amira Software for post-processing and visualization.

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Courtesy of Dr. T.Hildebrandt (Limmat Klinik, Zürich) and Zuse Institut Berlin

Courtesy of Pawan S Takhar, University of Illinois at Urbana-Champaign

Control of corn kernel drying process to avoid insect and microbial damage

Corn kernels have a complex structure, being composed of a pericarp layer outside while containing hard and soft endosperm and germ components. Corn kernels are harvested around 30% moisture content on dry basis and dried to about 12% moisture content using heated air. Drying helps to lower the water activity to increase their shelf life. If the drying is not controlled properly, the kernels develop stress cracks, which make them prone to insect and microbial damage.

Avizo Software’s advanced segmentation tools and meshing capability allow for FEA solver collaboration. Avizo Software helps study and control the drying process by allowing simulations on the real corn kernel geometry.

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Learn more about Avizo Software for food analysis

Cement paste characterization to understand properties of concrete or mortar

Cement powder consists of multi-size, multi-phase, irregularly shaped particles generally ranging in size from less than 1 µm to about 100 µm, with an average diameter of about 15-20 µm. Characterizing cement paste is important to understand the properties of concrete or mortar.

Avizo Software helps simulate the cement hydration process through advanced segmentation of the different phases, including the pore space. Avizo Software quantifies the pore space, characterizing tortuosity and permeability, for instance, and can generate a 3D mesh suitable for further FEA simulation.

Data courtesy of Visible Cement Dataset

Data courtesy of Professor Patrick PERRE, Barbara MALINOWSKA, Cyril BRETON, Laboratory LGPM, CentraleSupelec

Nickel foam lattice analysis

High conductivity, chemical stability, and mechanical strength are important characteristics for an efficient current collector. Nickel foam is a high-porosity, low-density, permeable material with typically 75–95% of the volume consisting of void spaces. It is used in a wide variety of applications in heat exchangers, energy absorption, rechargeable battery applications, and has also been applied to the study of supercapacitors.

Avizo Software provides a virtual lab for characterizing materials. Avizo Software’s fast and robust meshing capability allows for collaboration with simulation solvers for FEA analysis. Porous networks can be analyzed through pore network modelling tools, and material physical properties such as absolute permeability, electrical resistivity, thermal conductivity, and molecular diffusion can be simulated. Additionally, Avizo Software will compute displacement and strain maps on volume images acquired in a reference and deformed state using Digital Volume Correlation modules.

The solution of choice for meshing

The XWind extension for Amira-Avizo Software provides dedicated meshing capabilities for advanced simulation (FEA/CFD):

  • Generate high quality mesh with smoothed conforming interfaces and topology preservation directly from a labeled (segmented) image
  • Dedicated easy to use meshing workroom allowing creating mesh and  defining boundary conditions for CFD with advanced 3D visualization and inspection tools
  • Mesh any topology with any number of materials
  • Fast robust meshing engine for very large dataset (e.g. 2000 cube dataset can be meshed in couple of hours depending on topology)
  • Fine control over distribution of element size to mix refined and coarser areas with global optimization of mesh quality
  • Boundary layer (high quality within thickness)
  • Export to major solver’s format
  • Export DVC displacements calculated with the Amira-Avizo Software XDigitalVolumeCorrelation extension at the mesh boundaries to link experiment with simulation


User stories

Amira and Avizo Software are popular 3D data analysis applications, used daily by thousands of researchers and engineers worldwide.

Amira-Avizo user stories


2017 Nobel Prize in Chemistry

Congratulations to the winners of the 2017 Nobel Prize in Chemistry. Three scientists; Dr. Jacques Dubochet, Dr. Joachim Frank, and Dr. Richard Henderson, were awarded the prize for their developments within Cryo-Electron Microscopy.

We are extremely proud of what these researchers and the structural biology community have achieved.