Thermo Scientific Amira-Avizo Software and PerGeos Software versions 2021.1 roll out exciting new tools and enhancements.

Explore very large multi-channel and time series imaging data with the Xplore5D extension for Amira Software.

Thanks to accelerated innovations in microscopy, life scientists now have access to a growing suite of imaging tools and techniques. Used alone or in combination with one another, high-powered instruments give researchers new ways to study biomolecular activity and advance their respective scientific discoveries. Yet, the increase in adoption of microscopy techniques in life science research results in increased size and volume of the imaging data acquired.

This abundance of data challenges the memory limits of scientists’s workstations and requires imaging software that is optimized for handling such high-resolution, multi-channel, and time series imaging data.

The new Xplore5D extension for Amira Software allows cell biologists to interactively explore very large multi-channel and time series imaging data. It is powered by a unique, lossless compression technology and features a user interface dedicated to interactive navigation in multi-channel time series imaging data. Xplore5D addresses the growing challenges of handling large imaging data, helping life scientists improve productivity and enabling the build of meaningful answers to complex questions across all fields of biomedical research.

Learn more

Xplore5D

Enhanced Deep Learning capabilities

The 2021.1 release of Amira-Avizo Software comes with additions in Deep Learning capabilities:

  • Automatic labeling of multiple image features at the same time using multi-class segmentation
  • More neuron network models can be used, including Resnet, which has performance proven to be much higher with the same precision
  • Increased accuracy with same computation time in several challenging segmentation cases, such as 3D characterization of cell ultrastructures, which are key for precision therapy research
  • Generation of label maps (instead of probability maps) with the new Deep Learning prediction module
  • Multiple improvements in performance, usability, and customization capabilities that make this enhanced Deep Learning framework a cutting-edge tool for automated imaging data analysis
deep-learning-v3

Additional improvements

Amira-Avizo Software 2021.1 comes with several improvements in performance and quality of various features:

  • Significantly improved detection quality using Membrane Enhancement Filter
  • Visualization enhancements
    • More realistic Volume Rendering
    • More accurate Color Blending of multi-channel data
    • Colorwash module for LDA Ortho Slice
  • Optimization of Morphological Binary Operators
  • Normalize Grayscale module enhancement
Visualization Improvements

​Read the full Release Notes for Amira-Avizo Software

The Release Notes allow you to gather a deeper knowledge about this new version of Amira-Avizo Software. They include more technical explanations, compatibility notes, operating systems Amira-Avizo Software runs on, and a list of solved issues.

Read the full Release Notes for PerGeos Software

The Release Notes allow you to gather a deeper knowledge about this new version of PerGeos Software. They include more technical explanations, compatibility notes, operating systems PerGeos Software runs on, and a list of solved issues.


Amira-Avizo Software packaging updates

Amira-Avizo Software 2021.1 introduces an important update in edition and extension packaging. Amira Software and Avizo Software have been fully aligned, and several extensions have been integrated by default in each edition.

This new version introduces two main editions:

Amira-Avizo 3D Software and Amira-Avizo 3D Pro Software

The main updates include:

  • Avizo Lite Software becomes Avizo 3D Software, and Amira Software becomes Amira 3D Software
  • Avizo Software becomes Avizo 3D Pro Software, and Amira Software + XImagePAQ becomes Amira 3D Pro Software
  • XImagePAQ, XLVolume, XPand, and XPublisher are integrated in Amira-Avizo 3D Pro Software. They are no longer available as separate extensions.
  • The Amira-Avizo Software token subscription model has become a per-user packs model


What was new

Digital Volume Correlation reached the next level

With a set of new features, Digital Volume Correlation 2020.3 makes it easier and faster to compute the 3D full-field displacement and strain maps from a reference volume to a deformed volume. DVC 2020.3 introduces a unique pre-processing module to quantify the displacement and strain uncertainties from two repeat scans and to help you ensure the reliability of your DVC analysis.

User experience has been improved with local and global approaches now separated in dedicated modules. The mesh generation used in the global approach can also be called from a separate module. You can now speed-up and automate your incremental DVC analysis (local or global) on a series of deformed volumes to capture the mechanical history of your specimen. Two strategies are proposed to take into account the level of cumulated strains (small or large).

DVC 2020.3 offers many new post-processing tools:

  • One-click extraction of displacement vector and strain tensor components
  • One-click computation of the Green-Lagrange strain tensor from a displacement field Enhanced visualization tools for scalars and vectors; easy color mapping on volumes, meshes, and surfaces
  • Median filter computation to smooth the displacement field resulting from DVC global approach and to correct its spurious vectors
  • More conversion and export capacities, such as Excel spreadsheet format, are available for you to perform further analysis with Python codes, FE-solvers, etc.
  • New tutorials and enriched documentation will help you quickly get up-to-speed with these new features.
DVC Module

New EM Toolbox suite for automated processing of large image stacks

Large stacks of serial sections must be aligned and often require denoising and contrast enhancement. These actions are time-consuming and demand powerful hardware. EM Toolbox offers powerful algorithms, is easy to use, and is able to perform tasks in a reasonable time, no matter which hardware is available.

EM Toolbox offers:

  • Post-processing workflow for Large Image Stacks (LVA) (out-of-core processing)
  • Straightforward configuration and execution of the workflow
  • Workflow: slice alignment, including reduction of distortions; image denoising; and contrast enhancement
EM Toolbox

​Read the full Release Notes for Amira-Avizo Software

The Release Notes allow you to gather a deeper knowledge about this new version of Amira-Avizo Software. They include more technical explanations, compatibility notes, operating systems Amira-Avizo Software runs on, and a list of solved issues.

Read the full Release Notes for PerGeos Software

The Release Notes allow you to gather a deeper knowledge about this new version of PerGeos Software. They include more technical explanations, compatibility notes, operating systems PerGeos Software runs on, and a list of solved issues.

Scale bar

Amira-Avizo Software 2020.2 introduces a new 2D ScaleBar module that can now be used with any orthoslice and any type of data, including RGB images, multi-channel, or large data.

Scale Bar

Relabel By Track ID – Amira Software for Cell Biology

The Relabel By Track ID is a new module that allows you to relabel a Time Series of segmented objects to match their corresponding Track ID. This enables the visualization of the results of the object tracking step using Slices or Voxelized Rendering. The Object Tracking Tutorial has been updated to explain how to use this new module

Relabel By Track ID

Molecule DNA-RNA Visualization

This Amira Software module visualizes the typical ladder structure of double-stranded DNA or single-stranded RNA structures. Each strand consists of multiple nucleotides with four different base types (Adenin, Cytosine, Guanine, and Thymine for DNA; and Adenine, Cytosine, Guanine, and Urazil for RNA). The backbone part of the nucleotide will be shown as a strand with an elliptical cross section and the bases as elliptical cylinders with different patterns at the ends, called sticks.

Instead of the sticks, you can visualize the sugar rings of the backbone in combination with the single-ring pyrimidines or the double-ring purines of the bases. The module provides several coloring modes that color either the DNA/RNA specific properties or general molecular properties.

The DNA-RNA Visualization module is available under the Avizo Software XMolecular and Amira Software XMolecular extension licenses.

Molecule DNA-RNA Visualization

Visualization of DNA and secondary structures of a nucleosome.N. Lindow, D. Baum, M. Leborgne, H.-C. Hege (2019). Interactive Visualization of RNA and DNA Structures. IEEE Transactions on Visualization and Computer Graphics, vol. 25, no. 1, pp. 967-976.

New option: Multiple Hypothesis Tracing for module Trace Correlation Lines

This new option allows for more robust results to be obtained, especially in the context of dense fibers and low data contrast. Multiple Hypothesis Tracing, proposed in the module Trace Correlation Lines, is included in Amira Software XTracing and Avizo Software XFiber extensions.

Multiple Hypothesis Tracing

Tracing of Microtubules in electron tomography images, with and without Multiple Hypothesis Tracing. The orange volume rendering displays the correlation field, and colored tubes show the traced centerlines.
Friman, O., Hindennach, M., Kühnel, C., Peitgen, H.-O. (2010). Multiple hypothesis template tracking of small 3D vessel structures. Medical Image Analysis, 14:160-171.

​Read the full Release Notes for Amira-Avizo Software

The Release Notes allow you to gather a deeper knowledge about this new version of Amira-Avizo Software. They include more technical explanations, compatibility notes, operating systems Amira-Avizo Software runs on, and a list of solved issues.

​Read the full Release Notes for PerGeos Software

The Release Notes allow you to gather a deeper knowledge about this new version of PerGeos Software. They include more technical explanations, compatibility notes, operating systems PerGeos Software runs on, and a list of solved issues.

New look and feel

Amira-Avizo Software 2020.1 introduces a new look and feel based on dark, contrasting visuals. This new user interface offers a more modern appearance. For those using other Thermo Scientific electron microscopy applications, the user experience will be enhanced, as the look and feel is consistent across software suites. These enhancements provide better readability, which improves comfort by reducing eye strain. And they save energy, too. Additionally, support for 4K displays has also been greatly improved.

Amira Avizo GUI

ScaleBar

The 2D ScaleBar module has been enhanced to enable the display of bar length using the currently selected display unit, improving visibility regardless of image contrast.

Scale Bar

Read the full Release Notes for Amira-Avizo Software

The Release Notes allow you to gather a deeper knowledge about this new version of Amira-Avizo Software. They include more technical explanations, compatibility notes, operating systems Amira-Avizo Software runs on, and a list of solved issues.

Read the full Release Notes for PerGeos Software

The Release Notes allow you to gather a deeper knowledge about this new version of PerGeos Software. They include more technical explanations, compatibility notes, operating systems PerGeos Software runs on, and a list of solved issues.

Amira-Avizo Software Upgrades

Amira-Avizo Software and PerGeos Software 2021.1 are regular upgrades and will be provided free-of-charge to all users under valid maintenance. These new versions also bring many improvements and fixes to known issues.

Amira-Avizo Software and PerGeos Software 2021.1 will be available soon. Please contact us for more information.


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Products

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
Digital Rock Analysis

  • Support for multi-data/multi-view, multi-channel, time series, very large data
  • Two-Phase Flow Simulation
  • Dual Energy Computed Tomography (DECT)

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​

Services

Amira-Avizo-Introductory-training_1160x600

Introductory training

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

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

Amira-Avizo-advanced-training_1160x600

Advanced training

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

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

Amira-Avizo-Custom-Dev_1160x600

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.


Features

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

    Contact us

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