Search
Search
Thermo Scientific Avizo Software for Geology uses a combination of AI segmentation and traditional image processing to calculate porosity, create pore network models, map ganglia networks, and generate fluid simulations from microscopy data. It offers advanced automation to help you streamline repetitive sample analysis.
Avizo Software works well with computed tomography, FIB-SEM, rock core CT, and less common imaging methods like spectroscopy. Typical geology applications include maximizing oil and gas extraction, improving mining yield from ore, and studying carbon capture utilization and storage.
Pore space within shale rocks is very thin and measured in the micron or nanometer scale. To capture a representative region for measurement, plasma focused ion beam milling (PFIB-SEM) can be used to capture 3D regions considered large compared to conventional electron microscopy. Large, high-resolution volumes help disentangle the organic matrix and porosity from the shale.
Avizo Software can reconstruct FIB-SEM stacks of images into a volume. The image processing tools align data and remove artifacts, such as curtaining. The visualization engine provides stunning visuals of the data in 3D, color mapping volumes of interest.
Avizo Software also helps with data segmentation and analysis. To isolate the organic matrix, a combination of thresholding, top-hat, and marker-based watershed are employed when contrast is excellent. Deep learning methods are used for challenging samples with charging artifacts or heterogeneous features.
Ultimately, a volume fraction can be calculated to inform a larger study of the potential for extraction from the shale formation. In the shale example pictured here, the organic matrix was 2.80% of the sample.
3D representation of organic matrix and porosity within a shale specimen. Data from PFIB-SEM was segmented and displayed in Avizo Software. Nanoscale investigations of oil and gas-bearing rocks can indicate potential yield for traditional oil and gas extraction. Figure reproduced from Hall et al. 2018.
Rock imaging provides a digital twin for understanding pore space geometry and organics in oil- and gas-bearing rock and shale. The heterogeneity of real samples benefits from deriving representative elementary volumes from real microscopy data.
Using multiple imaging technologies combines the strengths of multiple systems. In this example, high-resolution FIB-SEM imaging of a mudstone shale was registered in Avizo Software with a corresponding region in micro-CT of the same sample. When combined with other techniques like optical thin sections, this method permits high-resolution pore and organic phase measurements scaled to a large field of view.
In this study, an Avizo Software segmentation of FIB-SEM data uncovered that the organic matrix was 16.5% and porosity was 4.8% percent. The micro-CT data alone was not able to see micro- and nano-porosity, illustrating the value of multiscale, multimodal microscopy for oil extraction.
Organic matrix segmented from FIB-SEM tomography of a mudstone shale in Avizo Software. Figure reproduced from Fogden et al. 2016.
Well logs corresponding to drilled cores provide a common source of direct evidence to evaluate the potential oil or gas yield from a geological formation. Both hydraulic fracturing and traditional oil pumping benefit from careful study of these logs by petrophysicists and geologists.
Direct study of drilled cores can complement well bore sensor logs. As the samples are precious and expensive to obtain, non-destructive imaging with CT and MRI is preferred. CT is not usually sensitive to elemental contrast, but with a dual energy CT (DECT) study, Avizo Software can be used to infer the materials from a database relevant to the sample.
For example, in this rock core imaged at two peak X-ray energies, the DECT method in Avizo Software was used to infer the majority rock type and density for every millimeter along the core's length.
3D split view of a carbonate rock core showing the majority element found on each tomographic slice along the core. This inference comes from dual energy computed tomography, which is an imaging method and computational technique done in Avizo Software. Data courtesy: Victor and Prodanovic 2017.
Carbon capture promises to help abate carbon released from burning traditional fossil fuels, but the technique faces technical and logistical challenges. It is not fully understood is how much material a previously extracted oil field can retain.
Researchers can emulate the conditions of carbon capture with rock samples in a lab environment by repeatedly flooding the sample with, for example, oil, brine used in hydraulic fracturing, and concentrated carbon dioxide.
By modelling the pore space directly from micro-CT imaging data, researchers were able to realistically measure oil-wet rock pore flooding dynamics in Avizo Software. Non-destructive imaging and re-imaging provided direct evidence of lowered ganglion connectivity and residual carbon storage—two desirable outcomes for carbon capture.
Pore-scale 3D models of an oil-wet rock under gas injection and water flooding conditions. These 3D models from Avizo Software are used to estimate how much carbon a depleted oil field could potentially store with carbon capture technology. Figure reproduced under CC BY 4.0 from Alhosani et al. 2020.
A proposed solution for reducing the carbon footprint of industrialization is to store some of that carbon as CO₂ in the same reservoirs initially used for oil production. Simply pumping materials into the ground may not be as effective as desired due to the gaseous CO₂ escaping the reservoir system over time.
By conducting flooding experiments of carbonate rocks with micro-CT, Avizo Software can be used to locate and measure disconnected ganglia that should be capable of long-term CO₂ retention.
In this study, a barrier region was identified that retains the non-wetting phase behind it. This promoted early disconnection and is thought to enhance CO₂ trapping efficiency. Studies like these are essential for realizing the capabilities or limitations of this climate change mitigation tool.
Segmented pore space with separated ganglia in Avizo Software. Two rock cores show the disconnection of ganglia after repeated imbibition. This indicates potential for additional carbon capture. Image courtesy of Nihal Darraj of Imperial College London.
Modern devices such as batteries and semiconductors rely on rare earth elements and other minerals that are not common in the Earth's economically minable materials. Heterogenous samples that contain compound grains are then interesting as they may contain trace elements that can then be targeted for mining.
Various types of spectroscopy are commonly employed to understand the composition of unknown samples. Recently, spectroscopy has been more commonly extended to a raster pattern to produce an image based on the spectroscopic method. These layered and dense images can be studied in Avizo Software as multi-channel fields.
For example, a laser ablation laser ionization time of flight mass spectroscopy (LALI TOF-MS) investigation of a complex grain in a core plug is shown here. Individual maps of minerals are combined for co-visualization and pattern detection in a way that isolated images or spectrograms may not reveal.
Highly multichannel spectroscopy data are co-aligned and displayed as an image in Avizo Software. Visual representation of composite grains in core plugs is imaged with LALI-TOF-MS to reveal critical minerals such as lithium and chromium. Sample courtesy Exum Instruments.
As an alternative to traditional mining like blasting or digging, in situ blasting can break up material into fine particles without as greatly introducing safety concerns of ground-pressure control. Later, leaching solutions are applied to the top of a blasted ore deposit and collected through a network of pipes through the force of gravity. Collectively, this approach reduces costs for extracting certain targets such as low-grade ore deposits.
Because blasting creates a range of particle sizes and distributions, it is useful to study how leaching fluid can filter around and through a variety of particle compositions. Micro-CT imaging and Avizo Software can be used to extract a pore network model that is used to determine the tortuosity and relative permeability of the sample along the direction of fluid flow.
In this example, six samples with different particle size distributions had a pore network model extracted from segmentation data produced in Avizo Software. A high concentration of fine particles reduced permeability and network connectivity.
Pore network models generated in Avizo Software displayed within six physical ore models. These particle models represent the potential for mining low-grade ore deposits by leaching ore from in situ blasted rock. Figure reproduced under CC-BY-4.0 from Liu et al. 2025.
Avizo Software provides tools for processing and analyzing complex 2D and 3D imaging datasets that help geologists and paraphysicists extract quantitative information about rock structure, mineral composition, and pore systems for geological interpretation. Key functions include:
Yes. Avizo Software segments features in 2D or 3D image data and provides measures and models based on these data. Request a trial license to see how it performs for your work and talk with our team of experts to discuss your needs.
AI methods are relatively new and can work for noisy or non-ideal images that traditional image processing methods may not handle well. Avizo Software includes both AI methods and image processing methods. Sometimes, the combination of these techniques enables otherwise difficult work to be done more efficiently. Learn more about AI capabilities in Avizo Software.
Yes. Avizo 3D Pro Software includes the AI Assisted Selection tool, which is a pre-trained AI model that works well for digital rock applications. Other pre-trained models are available for download using the built-in Xtras Installer. These tools can be browsed in the Xtra Library.
Viewing pore network models in Avizo Software requires the XPNM extension. Creating a pore network model also requires Avizo 3D Pro Software. Learn more about Avizo Software packages.
In 2025, the functions of PerGeos Software were integrated into Avizo Software. Some specific functions were placed under either an XCore Profile or an XModelling & Simulation extension, which you can learn about on this page. If you were a former PerGeos Software user and want to use Avizo Software, we advise that you request a trial license or contact us.
Avizo Software primarily works with image data. Traditional digital rock imaging includes whole core imaging, micro-CT imaging, 2D SEM, optical thin sections, and FIB-SEM tomography. Less common imaging methods can be opened, viewed, and analyzed in Avizo Software, such as 3D mass spectroscopy, MRI, ultrasound, and terahertz imaging. If you want to test Avizo Software, we advise that you request a trial license or contact us to validate whether your data are suitable for analysis in the software.
Yes. Avizo 3D Pro Software offers an extension called XLab that runs lattice Boltzmann method fluid dynamics simulations of flow. This is advantageous because the simulation is matched to the observed pore phase in your sample. It is then helpful to also do preprocessing and segmentation, such as with Avizo 3D Pro Software. Avizo Software offers powerful and dynamic 3D visualizations of the simulated fluid flow to aid in identifying how tortuous pathways are and the effective permeability of a sample. Those with the XModelling & Simulation extension can perform two-phase simulation as well. For more detail, review Avizo Software packages.
Yes. Avizo Software includes a dedicated Segmentation+ Workroom. The workroom provides complementary tools for labeling, such as a lasso, brush tool, watershed, and magic wand. This workroom allows users to generate ground truth for customized deep learning models that can be reused and transferred between Avizo Software installations.
It is recommended to have an NVIDIA GPU with CUDA support. There are other considerations shared with the rest of Avizo Software. Full hardware requirements are listed here and may change.
Thermo Fisher Scientific offers training sessions, video tutorials, webinars, and technical support to ensure you are using Avizo Software to its fullest capacity. It is recommended to begin with the Learning Center or the User’s Guide packaged with the software.
For Research Use Only. Not for use in diagnostic procedures.