Accelerate your imaging data processing, segmentation, and classification using Machine and Deep Learning in Amira, Avizo, and PerGeos Software

Artificial intelligence (AI) methods, such as machine learning and deep learning, have proven to be powerful approaches for automating image segmentation and improving image quality.

The use of AI-based tools in Thermo Scientific Amira-Avizo 2D Software, Amira-Avizo Software, and PerGeos Software is a major leap forward and enriches processing capabilities by allowing the ability to mix both traditional and AI-based algorithms.

Deep Learning in Amira-Avizo Software and PerGeos Software

Deep-learned neural networks have proven to be invaluable tools for many research and industrial purposes in recent years. Using deep learning for processing images allows researchers to go beyond traditional image processing for greatly improved results.

Amira-Avizo Software and PerGeos Software provide ideal environments for deep learning.

A rich image pre/post-processing toolbox supplementing user-friendly manual and supervised segmentation allows enhanced data annotation and preparation for the training phase and the prediction phase. It also leverages the actual model building, training, and prediction steps from experienced deep learning frameworks, such as TensorFlow and Keras. The workflow for learning from a manually segmented subset and performing the prediction on a complete data set is as simple as applying two modules.

Deep learning model trained on a subvolume for detecting membranes and mitochondria, prediction applied on the full volume. Data courtesy of Cardona A, et al. 2010. An Integrated Micro- and Macroarchitectural Analysis of the Drosophila Brain by Computer-Assisted Serial Section Electron Microscopy. PLoS Biol 8(10): e1000502. doi:10.1371/journal.pbio.1000502.

Deep Learning off-the-shelf

The Deep Learning Prediction module allows for trained models to be used on data. It can be incorporated within any workflow or recipe to automate your image processing, segmentation, or analysis tasks.


The deep learning training modules feature a highly configurable tool for training models using state-of-the-art architectures, such as Unet with Resnet or VGG backbones, data augmentation, a selection of loss, and metric functions. The training can occur from scratch (random weights) or from pre-trained weights.


The training is monitored in real time using TensorBoard to track metrics, such as loss and accuracy, or to visualize the model’s architecture.

Watch accuracy and loss on training and validation sets.

Customizable solution

Amira-Avizo Software and PerGeos Software’s latest versions provide a default set of deep learning Python packages and modules based on Keras, a high-level neural networks API running on top of TensorFlow. You can go further by customizing your Python environment or creating multiple self-contained Python environments with their own sets of packages and use them within your own Python Script Modules (pyscro).

Advanced users and Python programmers can customize both the Deep Learning Training and Prediction modules. A plugin system allows for the definition of custom model architectures, loss, or metric functions, which can be readily available from the GUI Deep Learning Training module.

Prediction can also be customized from pre- to post-prediction processing, to enable full control on the input and outputs and to optimize memory usage.

Applications and use cases

Image segmentation of mitochondria blobs

Mitochondria are difficult to segment using traditional approaches because they have connections with the outer endoplasmic reticulum and an internal membrane-like structure.

The model trained with Amira-Avizo Software’s deep learning tool allows the automatic extraction of mitochondria from a FIB-SEM stack. The training was done using only a few slices, which were segmented manually with Amira-Avizo Software’s segmentation editor. It was then possible to automatically segment the rest of the stack, saving hours of manual work.


(Left) Manual segmentation using Amira-Avizo Software's segmentation editor, and (right) 3D visualization of the mitochondria from the automatic segmentation of the full stack with deep learning. Data courtesy of Advanced Imaging Res. Center, Kurume Univ. Sch. Med.

Image denoising of SEM

For 3D serial sectioning and 2D tiling applications, time to data versus image quality must be carefully balanced. Usually, the data is heavily down-sampled to process it. Following acquisition, conventional algorithms, such as gaussian-smoothing and non-local-means filtering, leave artifacts. Alternatively, deep learning algorithms can be tuned in such a way that they do not induce artifacts. Processing can be done relatively quickly when a deep learning model is available. Below, we highlight a model that can quickly restore SEM images.

Image super-resolution

High-resolution images are often needed to clearly capture desired structural details, while lower resolution acquisition may be imposed by exposure time and dose applied to the sample.
Super-resolution deep learning algorithms can restore realistic details from lower resolution images, dramatically facilitating image segmentation.


Deep Learning segmentation of pores in solid oxide fuel cells in FIB-SEM

FIB-SEM 3D images of non-impregnated porous media suffered from a so-called pore-back effect, in which the back of a pore can be easily confused with a solid material lying on the section. In this case, we trained a deep learning model to recognize pore-backs by segmenting a number of image patches using traditional supervised techniques.

Illustration of the training of a deep learning model based on patches, including prediction on the full dataset. Solid Oxide Fuel Cell dataset courtesy of Sabanci University, Turkey.

Facies Classification with Supervised Machine Learning

Rock type (facies) identification plays a key role in the exploration and development of oil and gas reservoirs. Traditional core-based facies identification is costly, time consuming, and subjective. Machine Learning allows you to address the challenges in a fully automated and reproducible way.


Color Auto Classification based on machine learning

Based on machine learning, the Color Auto Classification tool automatically segments a color image into labels. A supervised random forest method is used.

Automatic segmentation of an optical image of a thin section using Color Auto Classification. Data courtesy of Stratum Reservoir.

Texture Supervised Classification based on machine learning

Texture classification is a machine learning technique that relies on learning texture patterns from markers defined by the user and then classifying each pixel of the image according to its similarity to the learned patterns.


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Thermo Scientific Amira 2D-5D visualization Software

Amira Software
Life Sciences

  • Explore 2D-5D bioimaging data
  • Identify and understand structures
  • Obtain statistical information
  • Share reports and stunning animations

Avizo Software
Materials Science

  • Support for multi-data/multi-view, multi-channel, time series, very large data
  • Advanced multi-mode 2D/3D automatic registration
  • Artifact reduction algorithms

Pergeos Software
Rocks and Minerals

  • Visualize, process, and analyze rock imagery data
  • Perform multi-scale imaging analysis from pore to core
  • Calculate geological and petrophysical properties

Athena Software
Imaging Data Management

  • Ensure traceability of images, data, metadata and experimental workflows
  • Simplify your imaging workflow​
  • Improve collaboration
  • Secure and manage data access​



Introductory training

Shorten your learning curve and maximize your investment with this introductory training specifically designed for new users of Amira, Avizo and PerGeos Software.

The course consists of a lecture with hands-on sessions. The training material highlights the basic features and functionalities of Amira, Avizo and PerGeos Software.


Advanced training

Maximize your investment and reduce your time-to-results with this advanced training specifically designed for existing users of Amira, Avizo and PerGeos Software.

The course consists of a lecture with hands-on sessions. The training material highlights advanced features and functionalities of Amira, Avizo and PerGeos Software.


Custom development

With over 25 years of experience in 3D and image processing and hundreds of custom projects delivered to organizations small and large, Thermo Fisher Scientific can provide you with a solution tailored to fit your specific needs.

We can customize and expand our software solutions at various levels.


Import and process your imaging data

    • Handle any modality, at any scale, of any size:

    - Bio-Formats
    - Bitmap formats
    - Microscopy: electron and optical
    - Medical and neuroimage formats
    - Molecular formats
    - Other acquisition devices (MRI, radiography, etc.)

    • Finite element modeling, geometric modeling, CAD
    • Support for multi-data/multi-view, multi-channel, time series, very large data
    • Scaling, calibration, conversion, re-sampling
    • Image enhancement, comprehensive filtering and convolution, Fourier frequency transforms
    • Artifact reduction algorithms
    • Advanced multi-mode 2D/3D automatic registration
    • Image stack alignment, arithmetic, correlation, fusion

    Easily segment your imaging data

    • Thresholding and auto-segmentation, object separation, automatic labeling
    • Region growing, snakes, interpolation, wrapping, smoothing
    • Morphological processing, including watershed and basins
    • Machine Learning-based segmentation
    • Automatic tracing of individual fibers and filaments
    • Skeletonization and filament network extraction
    • Interactive tools for generation or editing of segmentation and spatial graphs
    • 3D surface reconstruction
    • Grid generation for FEA/CFD


    Export your analysis and visualization work to seamlessly publish and present it

    • Animation and video generation
    • Advanced key frame and object animation
    • Mix images, geometric models, measurements and simulations
    • Annotations, measures legends, histograms and curve plots
    • Export spreadsheets, 3D models, high-quality images
    • Active and passive 3D stereo vision
    • Single and tiled screen display
    • Immersive environment

    Visualize and explore your imaging data

    • Interactive high-quality volume and multichannel visualization
    • Orthogonal, oblique, cylindrical and curved slicing
    • Contouring and iso-surface extraction
    • Maximum Intensity or other types of projections
    • Vector and tensor visualization
    • Objects and tracks
    • Molecular visualization

    Analyze your imaging data and obtain quantitative information

    • Intuitive recipe creation, customization, automated replay
    • Built-in measurements, including counts, volumes, areas, perimeters, aspect ratios and orientations
    • User-defined measures
    • Results viewer with spreadsheet tool and charting
    • Automatic individual feature measurements, 3D localization and spreadsheet selection
    • Automated statistics, distribution graphs
    • Feature filtering using any measurement criterion
    • Data registration, deformation, comparison and measurements


    Easily and quickly adapt Amira Software to your specific needs

    • Custom C++ modules development
    • MATLAB™ bridge
    • Python scripting API

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