What’s New in imaging-data visualization and analysis software

Wherever imaging datasets need to be processed and managed, Thermo Scientific software solutions offer state-of-the-art image data processing, exploration, and analysis features. Our adaptable software packages dedicated to life sciences, materials science, and digital rock analysis evolve regularly. New features, improvements, and new Xtras developed with scientific experts deliver best-in-class analytical software solutions tailored to your needs.

Amira Software, Avizo Software, and PerGeos Software version 2023.1 roll out exciting new tools and enhancements.

Further streamline your interactive segmentation pipelines with the new Segmentation+ Workroom
Get faster information from your data with new Deep Learning Denoising tools
Build recipes more quickly and easily with new options added to the Image Recipe Designer workroom

Process even larger datasets with the Digital Volume Correlation module
Enhance your simulation pipeline with the improved Meshing workroom
Simplify your work with new modules (Object Separation, Remove Islands)
Get support with new add-ons and how-to videos

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.

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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.

Noise2Void Deep Learning denoising applied to EM image of a zebrafish

Noise2Void Deep Learning denoising applied to EM image of a SOFC sample

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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

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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.

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.

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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.

Hierarchical watershed segmentation applied to a 3D microCT volume of a rock sample.

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.

How to receive upgrades

Regular upgrades including new features and enhancements are provided free-of-charge to all users under valid maintenance.

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

2022.2

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.

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.

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.

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.

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.

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

PerGeos Software release notes

Amira-Avizo2D Software release notes

2022.1

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

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

PerGeos Software release notes

Amira-Avizo2D Software release notes

2021.2

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.

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

High-performance Digital Volume Correlation made easier

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

Read the full Release Notes for PerGeos Software

2021.1

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

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

Read the full Release Notes for Amira-Avizo Software

Read the full Release Notes for PerGeos Software

2020.3

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.

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

Read the full Release Notes for Amira-Avizo Software

Read the full Release Notes for PerGeos Software

2020.2

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.

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

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.

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.

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

Read the full Release Notes for PerGeos Software

2020.1

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.

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.