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Tailored AI-enabled imaging solutions for life sciences
Image acquisition is only the beginning; true discovery starts when data becomes understanding.
Thermo Scientific Amira Software was created with life scientists in mind, combining advanced AI tools with intuitive design to transform complex imaging data into clear, quantifiable results.
By incorporating the criteria researchers use to interpret microscopy, CT, MRI, and other images, Amira Software’s AI tools enhance image quality, accelerate segmentation, and reveal structures that were once hidden in noise.
What Amira Software’s AI tools mean for you
Amira Software’s AI tools are built to make your imaging workflow easier, faster, and more insightful so you can focus on the science, not the software.
Accelerate discovery, save time
AI automation cuts routine processing from hours to minutes, delivering clear, quantitative results so you can validate findings faster and focus on discovery.
See more, get reliable results
AI delivers consistent, reproducible analysis while advanced denoising and segmentation uncover hidden structures and subtle details missed by traditional methods.
Work smarter, adapt faster
AI-assisted tools simplify complex workflows, no coding needed, and flexibly adapt to any imaging modality or research goal.
How Amira AI image analysis software supports the entire workflow
Amira Software integrates artificial intelligence (AI) directly into the imaging workflow: visualization, processing, segmentation, and quantitative analysis. Each step is powered by intelligent tools that enhance image quality, identify structures with precision, and extract meaningful data effortlessly, turning complex image analysis into a streamlined, intuitive process.
- Enhancement
- Segmentation
- Classification
Reveal clarity with AI-powered image enhancement
Amira Software’s AI-driven preprocessing tools turn challenging, low-signal or low-contrast datasets into high-quality images ideal for segmentation and quantitative analysis.
Unsupervised AI denoising (Noise2Void)
This is a universal denoising solution that requires no clean reference images, making it ideal for fast, effortless improvements on any imaging modality.
Supervised AI denoising (Noise2Clean)
Designed to accelerate acquisition workflows, this method uses a small number of paired noisy/clean slices to produce exceptionally sharp, high-fidelity results, even on extremely noisy data such as cryo-ET.
Pretrained AI denoising models
Get instant access to expertly trained models for specific imaging types, such as BSE-SEM, helping enable optimized results right out of the box.
Pan neuronal labelled head ganglion of C. elegans. Fluorescence Microscopy Image Denoising Dataset
Reveal structure with AI-powered segmentation
Segmentation is where Amira Software’s AI tools shines brightest, delivering fast, accurate, and robust structure detection even on the most challenging datasets.
AI-powered annotation tools
Simplify training data creation with intuitive tools like the brush, lasso, and AI-assisted selection. Annotate structures in just a few clicks, accelerating model preparation and improving reproducibility.
Flexible AI model training
Amira Software allows you to train models in the dimensionality that best fits the data:
- 2D: Fastest training, ideal for simple segmentation tasks
- 2.5D: Enhanced accuracy with minimal extra training time
- 3D: Highest fidelity, capturing full volumetric context
Cryo-ET membrane segmentation comparing 2D (A,C) and 2.5D (B,D) U-Nets, with the 2.5D model showing fewer segmentation artifacts and higher accuracy.
Shallow and deep learning architectures
Amira Software provides flexible AI architectures designed to match different levels of segmentation complexity. You can choose fast, lightweight models for simple tasks or more advanced networks when the data demands higher precision.
- Shallow networks—Quick to train, ideal for binary segmentation
- Deep networks—Captures subtle features, excels in noisy or complex samples
Model training, evaluation, and management
Train, evaluate, and manage AI models directly within Amira Software using accelerated workflows. Built-in metrics and the AI Model Manager make it easy to assess performance and retrain and automate workflows for consistent, large-scale data analysis.
Amira Software includes a full suite for evaluating and comparing models:
- Dice, Jaccard, precision, recall, and more
- Side-by-side visual comparisons
- Organized model library with export/import capabilities.
Pretrained segmentation models
Access ready-to-use AI models for 2D and 3D datasets. Start segmenting instantly without additional training or data preparation.
- CellPose and CellPose-SAM (2D/3D) provide advanced performance across cell types and imaging modalities
- Additional pretrained models covering light microscopy, electron microscopy, and CT
AI object classification and quantitative analysis
Turn segmentation into science with AI-driven interpretation
After segmentation, Amira Software gives you the power to extract meaningful scientific insights.
AI object classification
Automatically classify segmented objects by morphology, intensity, or texture. Quantify and compare different cell types, organelles, or material components to extract deeper biological or structural insight, enabling:
- Rapid phenotype screening
- Automated categorization of structural variants
- Clearer, more objective insights
Combined with Amira Software’s robust measurement toolkit (volume, surface area, interface quantification, time-series analysis), these AI features reveal new dimensions of understanding in your imaging data.
How Amira Software’s AI helps with image data analysis in Life Sciences
In this on-demand webinar, you’ll get a clear, practical look at how Amira Software uses AI to clean, annotate, and segment complex scientific images faster and with higher accuracy.
You will learn:
- How AI-powered and conventional denoising tools quickly turn noisy data into clear images
- How AI-assisted annotation speeds up ground-truth creation When to use 2D, 3D, or 2.5D segmentation for the best results
If you work with challenging microscopy, CT, or any imaging data, this session shows exactly how Amira Software can simplify your workflow and improve the quality of your results.
FAQ (frequently asked questions)
Core AI tools like denoising and segmentation are included with Amira Software 3D, while advanced features such as Cellpose or object classifications are available through Amira Software 3D Pro edition.
No coding or machine learning background is required. Amira Software’s AI modules are fully integrated into an intuitive, visual interface. You can train, evaluate, and apply models through guided workflows.
In most cases, just a few annotated slices (typically 2–5) are enough to train an accurate model. Amira Software’s deep learning networks are optimized for small datasets, reducing the time and effort needed for manual labeling.
Yes. Amira Software supports all major microscopy, EM, and CT data formats, and it integrates seamlessly into existing image analysis pipelines. AI tools can be combined with classical processing, visualization, and quantification steps in a single workflow.
Most models train in 30 to 60 minutes, depending on data size and hardware. Once trained, models can be applied instantly to large datasets, saving significant analysis time compared to manual segmentation.
Yes. Amira Software includes pre-trained models such as Cellpose variants for 2D and 3D segmentation. These can be used immediately or fine-tuned with your own data for more specific applications.
Amira Software provides built-in evaluation metrics and visual tools to compare model predictions with ground truth. This ensures that every analysis step is measurable, reproducible, and transparent.
They do. AI workflows in Amira Software are transparent, documented, and fully reproducible, which meets the standards of peer-reviewed publications. Researchers simply need to report their model type, training data, and evaluation metrics. Many published studies already include Amira Software-based AI segmentation as part of their imaging analysis.
You can find example datasets and ready-to-use workflows in the Amira Software Xtra Library. The library provides downloadable AI modules, sample data, and step-by-step workflows to help you explore Amira Software’s capabilities right away.
Yes. Amira Software’s AI Model Manager lets you export and import trained models, making it easy to share them with other users or labs. This promotes reproducibility and consistency across teams, ensuring identical analysis workflows even on different systems.
Absolutely. We offer training sessions, tutorials, webinars, and technical support to help you get the most out of Amira Software’s AI capabilities. Customized training can cover everything from setup to advanced workflow optimization. For more information, feel free to contact us.
Experience Amira Software
Struggling to interpret complex biological data? Amira Software makes it easier.
With AI-powered segmentation, visualization, and analysis tools, Amira Software transforms microscopy and life science datasets into clear, actionable insights faster and with greater accuracy.
Request a trial today and see how Amira Software can transform your data analysis.
For Research Use Only. Not for use in diagnostic procedures.