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Thermo Scientific Amira and Avizo Software have always delivered powerful segmentation features. Our new purpose-built Segmentation+ Workroom builds on that by addressing complex requirements from a wide range of data types and objectives.
Combining interactive, automated, and AI-based segmentation tools in a user-friendly interface, the Segmentation+ Workroom can be tailored to your specific needs to help you enhance productivity and streamline your workflow.
AI-supported image segmentation
The Segmentation+ Workroom uses cutting-edge AI-based tools for image segmentation that make it easy to handle complex datasets. Its precise AI algorithms automatically analyze and segment images to help you enhance speed, efficiency, and segmentation quality.
Designed with user accessibility in mind, our AI-based tools eliminate the need for extensive image processing expertise. Users of all skill levels can leverage the AI tools to segment various structures, regardless of size or shape. Advanced algorithms recognize and segment different material textures, enhancing accuracy and versatility. Within the workroom, you'll find all the necessary tools for annotating ground truth, streamlining your workflow without switching software or environments.
AI-assisted segmentation on chlamydomonas sample dataset
Lasso automatic image segmentation tool
The Lasso is a cutting-edge selection tool that outlines specific areas within an image in 2D and 3D. Its freehand drawing capability can help you create custom regions, streamlining detailed analysis. The tool accurately selects all pixels within the user-defined polygonal shape, making it particularly useful for irregularly shaped objects.
The tool includes game-changing advanced features, including the spline function, which precisely adapts to object curvatures, and the edge detection function, which automatically identifies and follows intensity contrasts at object boundaries. Plus, the tool can be combined with the masking tool to restrict pixel selection to a certain threshold.
This blend of flexibility and precision makes the Lasso tool an indispensable asset for image analysis.
Superpixel image enhancement tool
The Superpixel tool simplifies and enhances image segmentation by grouping pixels with similar parameters into superpixels, significantly accelerating the selection process and helping to ensure precision.
Unlike manual segmentation using the brush tool, there's no need to meticulously follow image boundaries — the Superpixel tool automatically captures them. By following image edges, the selection algorithm generates superpixels with comparable sizes. You can adjust the balance between superpixel size and image characteristics for optimal results.
Intuitive image segmentation
The Segmentation+ Workroom user interface offers an intuitive image segmentation experience with a comprehensive set of tools. It prioritizes efficiency, enabling a focused and uninterrupted workflow.
The layout was carefully designed to logically group features, ensuring easy accessibility. The data viewer in the center of the workroom seamlessly transitions between 2D and 3D. Interactive segmentation features and selection modifier tools are conveniently located above. Automated Advanced Segmentation Tools, including AI models, are positioned on the left side for easy access, but can be undocked and repositioned as needed.
Our segmentation tools are optimized for both high and low levels of zoom, allowing for swift segmentation at low magnification and precise segmentation when zoomed in.
Segmentation+ Workroom frequently asked questions
This function is still available. Simply right-click to “Select” any material.
AI-assisted segmentation tools are available in Amira and Avizo Software within the new Segmentation+ Workroom powered by deep learning. Once you install the Python Environment and Deep Learning packages at the first time of use, it will be ready to go.
Amira and Avizo Software versions 2024.1 and later can segment several phases at once.
More patches that contain annotated labels will yield a better result. You can try first with a few patches and repeat the same steps on newly generated labels to improve segmentation and prediction quality. We try to have patches that cover all background as much as possible to distinguish the features of interest from the background.
You can activate and deactivate the crosshairs displayed in 2D views by pressing the crosshair button 
to the right of the viewer mode buttons.
Once you have enclosed your desired region of interest with the Lasso tool, you can validate your selection by pressing the Enter key.
The current selection can be displayed in the 3D viewer by enabling the option in the bottom-right corner of the viewer.
Navigation is controlled by pressing Ctrl + Mouse wheel or Ctrl + Arrow keys when hovering over the 2D viewer you want to interact with. The scroll bar on the left side of the viewer can also be used to navigate between slices using arrow keys, the mouse wheel, the left click, or by typing the desired slice index.
Tutorials
Interactive image segmentation
AI-assisted cryo-EM segmentation
New features and enhancements
For Research Use Only. Not for use in diagnostic procedures.