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Amira Software, Avizo Software version 2024.1 introduce innovative AI features and improvements.

         


Amira and Avizo Software webinar

What’s new in Amira and Avizo Software

Live webinar | June 11, 2024
Session 1: 10:00 a.m. CET | 5:00 p.m. KST
Session 2: 5:00 p.m. CET | 11:00 a.m. ET | 8:00 a.m. PT

Join this live session and learn more about:

  • A new user guide designed to facilitate a smoother learning experience
  • Updates to the Segmentation+ Workroom that enhance robustness, ergonomics, utility, and intuitiveness
  • New AI-assisted tools, including multi-class support

Register now

         

         

New documentation

 

Introducing our brand new documentation and user guide, completely rewritten from scratch! The help system now opens in your default browser, so you can now enjoy multiple pages simultaneously without any window modality issues. We've simplified the presentation and improved navigation for a seamless experience. The guide is now written in easier-to-understand technical English, with new features like gifs and potential video integration. Readable formulas and convenient code boxes with a copy button make it easier to use. 

New documentation
Re-organized user guide is now displayed in your preferred web browser

         

         

Generate multi-class AI segmentation with ease

 

Our updated AI-assisted tool now offers an enhanced feature set to cater to your needs. With the latest version, you can generate a multi-class segmentation from a single sparsely annotated image within the Segmentation+ workroom. One of the key advancements of this update is the uninterrupted processing of all materials, resulting in a more seamless and user-friendly experience. The computation time and segmentation quality remain consistent, ensuring reliable and efficient results.

Moreover, our "Patch Extractor" module required for training deep learning segmentation models has been significantly improved. The module now supports extraction of multi-class patches from the grayscale and label images. This enhancement simplifies training of deep 2D UNet models using the “DL Training – Segmentation 2D” module, especially when working with sparsely annotated data.

Generate multi-class AI segmentation with ease
AI Assisted Segmentation Tool now process all materials and generates a label field as output

         

 

Enhanced Segmentation+ Workroom with exciting new upgrades

 

The newly enhanced capabilities and ergonomics in the Segmentation+ Workroom provide a seamless and user-friendly environment, helping you accomplish your segmentation tasks with greater ease and precision.

Magic wand live update

Experience enhanced flexibility and precision in voxel selection with our latest improvement to the Magic Wand. Now, when a seed voxel is selected, a new selection is automatically generated whenever you modify the range of the masking histogram. This cutting-edge feature empowers you to easily refine your voxel selection, ensuring the utmost accuracy.

New tutorial

Discover the power of the Interactive Threshold Tutorial, now available in the help menu. This innovative guided tour allows you to master the threshold tool with ease and confidence. Whether you're a beginner or an experienced user, this tutorial will take you step-by-step through the thresholding process, providing valuable insights and practical tips along the way. 

Threshold tool
New guided tutorial on the Threshold tool

Enhanced Lasso Tool – Smooth and Precise Shape Trimming

Experience the next level of precision and smoothness in shape trimming with the implementation of our advanced BSpline technology. This cutting-edge enhancement is designed to excel, particularly at low zoom levels, ensuring optimal trimming of shapes. Now you can enjoy improved accuracy when trimming round shapes, resulting in flawlessly refined contours. With this upgrade, you can achieve superior results with fewer control points, saving time and effort while maintaining exceptional precision. 

Enhanced Lasso Tool
left) Polygonal lasso right) Lasso with Spline constraint

New Menus

We are thrilled to introduce dedicated menus within our application, making it even easier for you to access the Selection and Segmentation tools. With this streamlined approach, these essential features are now conveniently located in their dedicated menus, ensuring a more intuitive and efficient user experience. 

New Segmentation Selection Menus

 

New automatic segmentation tools

 

The new tools in our Segmentation+ Workroom will help you achieve smoother material boundaries, streamline material selection, and efficiently merge materials.

Smooth label

Achieve smoother and more refined material boundaries in your label image with our modified Gaussian filter tool. This new feature allows you to apply a customized Gaussian filter, providing greater flexibility in modifying your current segmentation or generating a new label image. By adjusting the parameters of the filter, you can seamlessly enhance the smoothness of material boundaries, resulting in a more visually appealing and accurate representation.

Merge materials

Introducing a game-changing enhancement in our Segmentation+ Workroom: the ability to effortlessly merge materials directly from the "Material List." This upgrade revolutionizes your segmentation workflow, simplifying and streamlining the management of materials in your projects. With just a few clicks, you can now seamlessly merge materials, saving valuable time and ensuring a more efficient segmentation process. 

Pick tool

Experience the power of our enhanced Pick tool, designed to simplify and streamline the material selection process. With this latest update, you can now choose to select either an entire material or a single connected component independently, whether it's on the current slice or in the 3D view. This newfound flexibility provides greater control and convenience, allowing for more precise and efficient material selection. 

Merging Materials
Select structures in the 3D viewer using the Pick tool. Use the Quick Probe to identify material names, and merge materials when automatic segmentation pipeline resulted in over-separation. Data courtesy of Mark Kenney, University of Rochester Medical Center (https://doi.org/10.1016/j.bonr.2022.101167)

 

Achieve higher flexibility and accuracy with probability maps in the Deep Learning Prediction Module

 

When utilizing AI segmentation models, you now have the flexibility to select the desired prediction format, either as a label image or a probability map per class. Probability maps in AI image segmentation offer detailed information about the likelihood of each class at every pixel. By starting with probability maps, advanced users can enable uncertainty estimation, perform more nuanced analysis and design optimized post-processing recipes to improve the accuracy of their workflow.

 

 

 

Expansion of DVC mechanical regularization

 

Experience the power of our expanded mechanical regularization feature, designed to enhance your DVC (digital volume correlation) analysis. With this update, you can now leverage mechanical regularization within the DVC Uncertainty Measurement module, helping you optimize the balance between spatial resolution and measurement uncertainty. This advanced capability ensures more accurate and reliable results, regardless of the sample type being analyzed.

Furthermore, our mechanical regularization feature can now be applied to time series data within the Incremental Global DVC module. This breakthrough advancement allows for improved accuracy and reliability when analyzing dynamic or time-dependent samples.

To learn more about DVC capabilities in Amira and Avizo Software, please refer to release’s notes of version 2023.2 or the on-demand webinar accessible via our website.

 

Expansion of DVC mechanical regularization
DVC mechanical regularization helps to reveal displacement and strain for data with poor texture

         

         

         

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Our team of experts is always available to answer any questions you may have or discuss your project to support you in your research and discovery workflows.

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Amira-Avizo Software and PerGeos Software release notes

Read technical explanations, compatibility notes, operating system requirements, and a list of solved issues in the latest versions of Thermo Scientific Software.

​Amira-Avizo Software release notes

The release notes help you gather a deeper knowledge about this new version of Amira and Avizo Software. They include more technical explanations, compatibility notes, operating systems the software runs on, and a list of solved issues.

PerGeos Software release notes

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-Avizo2D Software release notes

The Release Notes allow you to gather a deeper knowledge about this new version of Amira-Avizo2D Software. They include more technical explanations, compatibility notes, operating systems Amira-Avizo2D Software runs on, and a list of solved issues.


How to receive upgrades

Users who have a valid maintenance plan are granted the advantage of receiving regular upgrades at no extra cost. These upgrades encompass not only bug fixes and security patches but also introduce new features and enhancements to improve the overall user experience. By keeping the software up-to-date, users can minimize the risk of obsolescence, ensure compatibility with upcoming operating systems, and maximize the capabilities of their software license.

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What was new in prior Amira, Avizo and PerGeos Software versions

 

Segmentation+ workroom is now ready to accelerate your interactive segmentation of even very large datasets

 

Since the previous 2023.1 version, important final enhancements have been added, making this 2023.2 version of Segmentation+ workroom complete and fully ready to empower your most demanding segmentation projects.

 

Guided tutorial for Segmentation+ workroom
Guided tutorial for Segmentation+ workroom.

Ergonomics:

  • Automatic Field Population upon entry
  • Rename and delete images or patch sets
  • Viewer layout preservation
  • Simplified viewer context menu
  • Interactive in-app tutorials

Navigation:

  • User-friendly crosshair navigation for seamless viewing across four panels.
  • Zoom under cursor in 2D/3D viewers, enhancing precision and interaction flexibility.

Interactive segmentation tools:

  • Default polygonal 2D lasso with control point placement and improved zoom precision.
  • Fixed brush performance issues with adjustable maximum.
  • Select only current material option in Top Hat, Threshold tools.
  • Improved Magic Wand with visible seed selection in 2D viewers and masking histogram.

Elevate your convex object segmentation with StarDist’s precision and efficiency

 

StarDist offers a seamless pathway to efficient AI-powered segmentation of convex objects. The specialized training modules, "DL Training Stardist 2D" and "DL Training Stardist 3D," are designed to cater to your specific needs. Once trained on small parts of your grayscale image data, these models excel in delivering precise object segmentation and seamless separation. This is achieved within our "Deep Learning Prediction" inference module, your trusted tool for accurate AI segmentation. Whether you are dealing with various types of particles in material science or exploring the structures of biological tissues, StarDist ensures rapid and pinpoint analysis of your data. Discover a new level of efficiency and accelerate your research with this exceptional tool.

2023-2-Avizo-4Square_1024x576
Pt/Pd catalyst nanoparticles on carbon acquired from Thermo Scientific Apreo SEM using 2D StartDist segmentation training and prediction.

 

Access the Xtras library directly from Amira-Avizo Software applications

 

The new Xtra Installer offers the convenience of browsing and installing Xtras directly from within the software, eliminating the need to download, unpack, and install them manually online.

You can now access the web experience and installation with just one click through a new menu item.

2023-2-Python-Command-Mod_1024x576
Install the Xtra from the software. A confirmation is displayed and an indication of the newly available modules is provided.
2023-2-Xtra-Load-UI_1024x466
New modules installed through Xtras are visible in the module menu in the Xtra category.

Learn how mechanical regularization enhances DVC module precision, making it compatible with finer elements and materials of lower resolution

 

The "Global DVC module" has been enhanced with a robust mechanical regularization method, allowing it to operate effectively with materials of lower resolution or signal-to-noise ratio. This enhancement also provides the flexibility to reduce the support grid size for improved precision in results.

This regularization can be thought of as a "mechanical filter" that reduces measurement uncertainties and surpasses traditional spatial resolution limits when dealing solely with texture. By applying an elastic assumption to displacement field measurements, DVC can now be applied to a wider range of materials, compensating for the challenges posed by poor microstructural texture, noise, and artifacts. Additionally, regularized DVC allows for finer meshing around material interfaces and cracks, enabling better capture of strain concentration..

2023-2-Amira-4Square_1024x576
DVC mechanical regularization applied to crack propagation during a wedge splitting test on a concrete specimen. Data courtesy of P. Carrara, ETHZ. A. Mishra, P. Carrara, M. Griffa, L. De Lorenzis, (2023) Fracture in concrete: in situ X-ray tomography tests, digital volume correlation, and phase field modeling. DOI: 10.3929/ethz-b-000633761

Discover the process of pixel extraction at the junction of three distinct materials

 

In fuel cell technology, triple phase boundaries (TPB) are crucial linear interfaces where three phases intersect, enabling electrochemical reactions. The TPB density, a vital metric for cell efficiency, can be quantified using the newly introduced "Triple Phase Boundaries" module, which extracts a spatial graph representing TPB from surfaces. To obtain the total TPB length, you can subsequently employ the "Spatial Graph Statistics" module.

2023-2-Materials-4Square_1024x576
Triple phase boundary extraction on FIB-SEM images of SOFC sample, with derived characteristics. Sample courtesy of Northwestern University.

 

New module: Molecule Cloud View

 

The "Molecule Cloud View" module allows you to visualize a group of molecules as their respective van der Waals surfaces within 3D datasets, specifying their positions and orientations. To use this feature, you need a molecule template, such as one from the Protein Data Bank, that encodes the molecule's structure, along with a table containing the X, Y, and Z coordinates, as well as orientation angles for each molecule.

 

Experience the Animation Director enhancements

 

The Animation Director now achieves superior movie quality with minimal file size, thanks to efficient codecs compatible with popular players like Windows Media Player and Microsoft PowerPoint. We've streamlined the movie creation interface, focusing on essential parameters, and introduced an advanced mode for less common functions like anti-aliasing rates or stereoscopic modes.

Amira-Avizo Software and PerGeos Software release notes

Read technical explanations, compatibility notes, operating system requirements, and a list of solved issues in the latest versions of Thermo Scientific Software.

​Amira-Avizo Software release notes

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.

PerGeos Software release notes

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-Avizo2D Software release notes

The Release Notes allow you to gather a deeper knowledge about this new version of Amira-Avizo2D Software. They include more technical explanations, compatibility notes, operating systems Amira-Avizo2D Software runs on, and a list of solved issues.

Further streamline your interactive segmentation pipelines with the new Segmentation+ Workroom

 

The Segmentation+ workroom takes interactive segmentation to a new level with support for larger datasets. The Segmentation+ workroom represents a major effort we have been undertaking for the last few releases to propose a brand new experience and lay the ground for exciting future innovations. We are continuing to enhance our new Segmentation+ workroom by porting popular tools from the classic segmentation editor, such as the Lasso tool, and by adding new technology and workflows such as Materials Selection to enhance the overall user experience in interactive segmentation.

segmentation-wr-Image-1024x576

Get faster information from your data with new Deep Learning Denoising tools

Denoising enhances image quality and facilitates accurate interpretation and analysis by reducing unwanted noise. Denoising modules help you run faster acquisitions while maintaining the quality needed for visualization and segmentation. In this release, we introduce the Noise2Void approach, an unsupervised denoising method that does not require noisy image pairs or clean target images. Therefore, a model can be directly trained with this method using images you want to denoise without the need for ground truth. A new deep learning module is now available to train a model using this pipeline. We will continue to expand and enhance our deep learning pipelines in future releases.

N2V-ZebraFishEye-Image-1024x576
Noise2Void Deep Learning denoising applied to EM image of a zebrafish
N2V-SDFC-Image-1024x576
Noise2Void Deep Learning denoising applied to EM image of a SOFC sample

Build recipes more quickly and easily with new options added to the Image Recipe Designer workroom

 

Not everyone is an image processing expert, which is why we introduced the Image Recipe Designer workroom in our previous release to help you quickly and easily design recipes that can be re-used and shared to streamline and reproduce image processing workflows. This version introduces new options to better document Image Recipes and facilitate their use, allowing better collaboration with recipes.

  • Documenting Image Recipes
  • Image Recipe Designer User Interface
  • Use your image recipes directly from the Module Browser
  • New modules exposed in Image Recipe Designer
IRD-Workroom-Image-1024x576

Process even larger datasets with the Digital Volume Correlation module

 

Digital Volume Correlation (DVC) is a valuable technique that enables quantitative analysis of deformation, non-invasive characterization, multiscale investigations, and applications in biomechanics and materials science. It contributes to the advancement of our knowledge in various fields and has implications for both research and clinical settings. As DVC is becoming more popular, datasets are getting larger and require an increasing computational demand. We’ve added to this version a multidomain approach and two new modules for mesh splitting with limited hardware requirements and for deformed volume correction.

DVC-Mod-Image-1024x576

Enhance your simulation pipeline with the improved Meshing workroom

 

Creating and exporting quality meshes is essential for many workflows involving simulation, but the process can sometimes be difficult and time consuming. We have significantly improved the performance and accuracy of our meshing workroom, as well as the Generate Tetra Mesh module, by providing granular control in mesh making and by using more self-explanatory language for existing functionalities. The speed and robustness of the meshing process is therefore enhanced. Further, the XWind extension is now available on Linux as well as Windows, providing more flexibility in the platform of choice.

ImpMeshing-WR1-Image-1024x576
ImpMeshing-WR2-Image-1024x576

New modules

Improve your segmentation with the new Hierarchical Watershed Segmentation module

 

Segmenting images into meaningful regions can be time consuming and complex on challenging datasets and could require complex pipelines to be created. Thanks to this new module, object separation becomes easier and more accurate by using the powerful watershed algorithm, a versatile technique that provides accurate and robust image segmentation. With this module, segmentation becomes much more interactive. Results are immediately updated based on the change of parameters without the need to recompute the full dataset.

HWS-Mod1-Image-1024x576
Hierarchical watershed segmentation applied to a 3D microCT volume of a rock sample.
HWS-Mod2-Image-1024x576
Hierarchical watershed segmentation applied to 3D EM image of a zebrafish embryo

Get better label images with Remove Islands

Sometimes label images require some final tweaking to be relevant. This module supports post-processing of label images by easily removing “islands,” which are connected components containing a number of voxels less than or equal to a specified value.

New add-ons and how-to videos

The following Xtras have been published or updated since the previous releases:

Xtras Installer: Provides an easy way to find and install resources from the Xtra Library on your local machine.

Iterate Recipe: Runs a given recipe while varying a chosen parameter value of any of the modules making up the recipe.

Surface Material Grid View: Arranges all materials of a surface in a grid view.

AI Assisted Tool for Cryo-EM Segmentation: Provides a tutorial to interactively segment a cellular cryo-electron tomography image using the AI-assisted segmentation tool in the Segmentation+ workroom.

Python Command Module: Enters and executes Python code from the Amira-Avizo Software interface.

Hough Circle Fitting (Update): Uses the Generalized Hough-transform to detect circles in an image.

These add-ons and short video tutorials will improve your productivity in daily tasks or in several specific analysis workflows, and we encourage you to regularly visit our XTra Library to stay on top of your productivity with Amira, Avizo, and PerGeos Software!

This release contains other enhancements and addresses several known bugs and limitations. Read the full Release Notes for more detailed information.

 

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Amira-Avizo Software and PerGeos Software release notes

Read technical explanations, compatibility notes, operating system requirements, and a list of solved issues in the latest versions of Thermo Scientific Software.

​Amira-Avizo Software release notes

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.

PerGeos Software release notes

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-Avizo2D Software release notes

The Release Notes allow you to gather a deeper knowledge about this new version of Amira-Avizo2D Software. They include more technical explanations, compatibility notes, operating systems Amira-Avizo2D Software runs on, and a list of solved issues.

Simplify your analysis workflows with
Image Recipe Designer & Player

 

Amira-Avizo Recipes are “packaged” workflows that automate a series of processing steps. These Recipes can be created and edited using what were formerly called “Image Stack Processing” (ISP) and “Image Volume Processing” (IVP) workrooms but are now unified in a single, dedicated Image Recipe Designer Workroom. The Image Recipe Player module allows users to run these Recipes within any global data-to-result workflow, providing a unique productivity tool to accelerate microscopy image-based research.

Recipe-Designer

Automatically process very large (out-of-core) datasets

 

The new Recipe technology now allows users to process out-of-core datasets. Today’s advanced microscopy systems, such as Lightsheet microscopes, produce very large, multichannel, time series image data. These datasets often do not fit within the available computer memory and are therefore very challenging to process. With this new 2022.2 release, Recipes can now be applied on these very large out-of-core datasets, allowing an unprecedented level of image data processing capability, and thus supporting the most demanding needs of scientific research and industrial applications.

SMS-in-Recipe-Designer

Accelerate interpretation of challenging datasets
with AI-assisted segmentation

 

Some complex imaging data can be very tedious or challenging to segment, requiring expert’s eyes and dozens of hours of manual operations to label the features of interest. The new AI-Assisted Segmentation tool available in this 2022.2 release provides an interactive, smart approach to accelerate the segmentation process. It performs most of the work automatically from a tiny part of the image annotated by the user, then replicates this segmentation on the entire image and generates a global selection that can be then edited before labeling the material.

It is particularly well suited for speeding up the processing of Electron Microscopy images but can also be used with any 3D dataset.

This new AI-assisted segmentation tool is available from the new high-performance segmentation+ workroom.

AI-Segmentation

Further explore high-performance segmentation
with enriched Segmentation+ workroom

 

The previous 2021.2 Amira-Avizo release introduced a brand-new high-performance segmentation workroom: Segmentation+.

In this new release, many classical segmentation tools available in the Classic Segmentation Editor have been added to the Segmentation+ workroom, including Magic Wand, Watershed, morphological operators, extended undo/redo capabilities, and more. Many improvements have been also brought to Segmentation+ in terms of user experience by picking, parameter tuning, lock/unlock feature. Some innovations including our new AI-assisted segmentation tool are also available from the Segmentation+ workroom.

Segmentation+

In the upcoming Amira-Avizo releases, all other important segmentation tools will be added to Segmentation+ to make it feature-complete. We will also propose, as we have done with this and our previous release, new innovative tools which will only be available from the Segmentation+ Workroom. While it may not be feature-complete yet, we encourage you to continue to use it on some challenging datasets and to give us your feedback on capabilities and usability!

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Boosting image-to-simulation workflows

 

The unique Amira-Avizo Meshing Workroom enables generation of 3D image-based mesh geometries suitable for Finite Element and CFD. The global performance of the meshing algorithm has been greatly enhanced, with doubled computation speed and better quality of generated meshes. As well, interoperability with major CAE/CFD/FEA software tools has been improved and now includes support for ABAQUS 2022, ANSYS 2022 and COMSOL 5.6 file formats among others.

Meshing-workroom

Other improvements, new add-ons and How-To videos

Various improvements also come with this Amira-Avizo 2022.2 release, including a new Patch Extractor module for faster AI annotations, enhanced user experience for the Beam Hardening Correction, Ring Artefact Removal and Cylindrical Intensity Profile modules, as well as 32-bits integer images support in the XPlore5D very large data extension, and more!

Finally, this Amira-Avizo 2022.2 release comes with lot of new XTras, including add-ons for more efficient or easier object separation, image stack creation, object extraction, surface area calculation, automated volume operations, and more.

As well, the XTras Library provides numerous new video ‘How-Tos’, including how to install Deep Learning Python environment, how to divide full data volume into sub-volumes for label analysis, and more.

These add-ons and short video tutorials will improve your productivity in daily tasks or in several specific analysis workflows, and we encourage you to regularly visit our XTRra Library to stay on top of your productivity with Amira, Avizo and PerGeos Software!

This release also addresses several known bugs and limitations. Read full Release Notes for more detailed information.

Amira-Avizo Software and PerGeos Software release notes

​ Amira-Avizo Software release notes

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.

PerGeos Software release notes

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-Avizo2D Software release notes

The Release Notes allow you to gather a deeper knowledge about this new version of Amira-Avizo2D Software. They include more technical explanations, compatibility notes, operating systems Amira-Avizo2D Software runs on, and a list of solved issues.

The Segmentation+ workroom evolves in Amira Software and Avizo Software

The goal of segmentation is to simplify and/or change the representation of an image into something that is more meaningful and easier to analyze. More precisely, image segmentation is the process of assigning a label to every pixel in an image in a way that pixels with the same label share certain characteristics. To this end, Avizo Software contains a segmentation workroom, and since 2021.2 we have introduced a new version called Segmentation+ workroom. We are continuing to add tools and new features to enrich it.

Superpixel

The new Superpixel tool allows you to brush and select “superpixels” (groups of smart pixels) and create a voxel selection out of them. It will dramatically increase the speed and accuracy of your selection. Compared with the former tool, the Superpixel brush lets you “paint” much faster without having to precisely follow the contours of your selection.

Threshold

Threshold tool has been available in our Classic workroom for some time and is now ready to use in our new Segmentation+ workroom. This tool allows you to create a voxel selection from a threshold range, either in the current slice or in 3D.

Interpolate slices

The Interpolate tool allows you to interpolate the selection between parallel slices. You can segment only a fraction of the slices within your dataset. This new implementation in the Segmentation+ workroom is based on the same algorithm used in the Classic Segmentation workroom and has been enhanced to affect both Segmentation workrooms. This tool allows increased productivity of highly manual segmentation cases, handled with tools such as brush, Superpixels or Threshold. Thanks to the new acceleration, the tool performs significantly faster than before (3 to 4 times faster on a 12-core CPU).


New deep learning modules for segmentation in 2D and 3D in Amira Software, Avizo Software and PerGeos Software

Faster segmentation in 2D through single large 2D data slice tiling.

A new module called “DL Training - Segmentation 2D” is now available for 2D image-based deep learning model training. With it, tiling is now possible.

The tiling functionality allows you to automatically split a single large 2D data slice (input data) into tiles (multiple sub-slices of the same size), each tile being considered as an independent training sample. In addition, it is now possible to randomize the order of the training samples before assigning samples in training and validation sets.

Increase quality of your segmentation in 3D

A new module called “DL Training - Segmentation 3D” is now available for 3D image-based deep learning model training. As with “DL Training - Segmentation 2D,” this new module relies on 3D convolutions rather than 2D for ResNet and VGG-backboned U-Nets and generic U-Nets.

The tiling functionality splits the input volume into independent training samples.This new module allows training 3D models that better account for 3D object shapes, and better prediction results quality can be expected.


Better segmentation of 3D non-spherical objects in Amira Software, Avizo Software and PerGeos Software

The new Random-Walk Distance Map module computes a distance map from binary segmentation, reflecting for each foreground voxel the average time it takes to do a random walk from this voxel to a background voxel. Compared with Euclidean or Chamfer distance maps, this module is less affected by noise in the segmentation or objects of anisotropic shapes. It is therefore particularly well-suited for object separation workflows in the case of non-spherical objects and/or noisy segmentation data.

Xplore5D extension evolves in Amira Software

SMS-Workflow-whatsNew

Enhanced user experience for large data conversion to SMS format

The SMS Converter is a tool embedded in the Amira Software Xplore5D extension, designed to easily and rapidly convert customer datasets into Thermo Fisher Scientific custom Out Of Core file format: SMS. The conversion step of your data is now guided and interactive.

New file formats supported

For users' convenience, the Xplore5D SMS Converter now supports a wide variety of file formats such as .tif, .tiff, .cif, and many others, thanks to the Bio-Formats third party library that provides more than 150 different formats. Using Bio-Formats, the SMS Converter supports single file multichannel datasets, single file time-series datasets, and single multichannel time-series datasets.

Quantitative analysis in ISP and IVP recipes

The following modules can now be used within the ISP and IVP workrooms and recipes:

  • Label Analysis
  • Global Analysis
  • Sieve Analysis
  • Analysis Filter

When you select a spreadsheet associated with one of these modules, the viewer will display the contents of the spreadsheet. Thanks to the addition of analysis modules directly in your recipes, you will be able to further automate your analysis and create more comprehensive recipes. You are now able to create recipes that embed all steps from image processing to quantification of individual objects and export the resulting spreadsheet.

Camera Bookmark, a new visualization module in Amira Software and Avizo Software

The versatility of the Camera Bookmark allows you to easily design your visual inspection scenarios, and with the ability to use them in animations, you will maximize the impact of the features you want to highlight through visual exploration of your data.

​ Amira-Avizo Software release notes

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.

PerGeos Software release notes

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-Avizo2D Software release notes

The Release Notes allow you to gather a deeper knowledge about this new version of Amira-Avizo2D Software. They include more technical explanations, compatibility notes, operating systems Amira-Avizo2D Software runs on, and a list of solved issues.

Road to next-generation workroom: high-performance segmentation of large data sets

With the widespread adoption of high-performance imaging systems, the file size of the imaging data is constantly increasing. As a result, segmenting and interpreting very large data is becoming a challenge.

The 2021.2 release of Thermo Scientific Amira-Avizo Software introduces the first version of our next generation segmentation workroom, Segmentation+.

This new workroom is based on an innovative technology and user interface that supports interactive segmentation of large image data and an unlimited number of material labels which can be organized into groups. With this initial release, the Segmentation+ workroom delivers performance improvements by a factor of three to five on 16k*16k 3D image data segmentation.

The first version of the Segmentation+ workroom includes a Brush Tool for segmentation, but newer versions will be equipped with additional segmentation tools and features.

The Classic Segmentation Editor with all the tools you know remains fully available and you can switch between both tools at any time.

Amira-Avizo segmentation+

High-performance DVC made easier

The Digital Volume Correlation (DVC) tool available in Amira-Avizo Software allows you to compute 3D full-field displacement and strain maps from volume images acquired during the deformation process of an object. DVC is an innovative, powerful contactless, bulk strain measurement technique in experimental mechanics, materials science, and biomechanics.

Amira-Avizo Software offers a truly unique and complete high-performance DVC solution. One of its main differentiators is the availability of the ‘Global Approach’ which allows for high-precision measurement of deformation phenomena.

As a first step, this Global Approach requires building a 3D mesh that conforms to the 3D shape of the object. Building such a high-quality continuous, homogeneous mesh requires some expertise and several manual steps.

The 2021.2 release of Amira-Avizo Software introduces a high-performance meshing technology that dramatically reduces the time and the complexity to build a high-quality mesh, ideal for the Global DVC Approach. 

This offers full access to a complete and powerful DVC solution even for non-expert users. 

Learn more about Digital Volume Correlation for Amira-Avizo Software

Amira-Avizo Software improvements and new add-ons

Various improvements come with this Amira-Avizo 2021.2 release, including enhancements to the newly released XPlore5D extension for multi-channel and time-series visualization, enhancements to the Python API, a major update of the BioFormats library, multiple enhancements to the MRC reader, and more.

Amira-Avizo 2021.2 also offers many new how-to’s video tutorials that will improve your productivity in several analysis workflows, such as advanced use of Colormaps, efficiently registering and merging images, fully benefiting from the automation capabilities of the Image Stack Processing workroom, and more.

This release also addresses several known bugs and limitations


Amira-Avizo Software and PerGeos Software release notes

​ 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.

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

​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.

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.


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Products

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​

Services

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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.

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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.

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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.



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