Powerful, multifaceted 2D–5D software for visualization, processing and analysis of microscopy imaging serving drug discovery

Supporting scientists and imaging experts on the challenging path toward drug discovery need state-of-the-art, repeatable, and automated 2D/3D software solutions. Thermo Scientific Amira Software reduces manual steps in the drug discovery process while increasing accuracy, time, and cost-effectiveness. From target discovery to compound identification, Amira Software is a powerful, multi-faceted 2D-5D platform for visualizing, manipulating, and understanding life science research data from many image modalities, including CT (Computed Tomography), MRI (Magnetic Resonance Imaging), 3D microscopy, and other techniques. It offers a comprehensive toolbox of image processing methods that can be automated through custom detection workflows.

Life science researchers continue to drive drug discovery and academic research down to a structural, sub-cellular level using automated, all-in-one tools and technologies. In pushing these limits, scientists can better understand how cells function and respond to disease or genetic variations, using their findings to advance research and development for breakthrough drug discoveries.

Imaging data

Amira Software workflow

Processing

Amira Software workflow

Visualization

Amira Software workflow

Analysis

Amira Software workflow

imaging data analysis toolbox

Empower your lab with powerful and comprehensive imaging data analysis toolbox

Amira Software offers high-end processing, registration, segmentation, visualization, animation, and data analysis to support your advanced discovery workflows in pharmaceutical research areas ranging from structural and cellular biology to tissue imaging, neuroscience, preclinical imaging, and bioengineering.

Accelerate time to data and time to market

Accelerate time to data and time to market

By providing ready-to-use recipes and AI-powered automated processing tools, Amira Software supports faster image analysis reducing the number of manual steps. The software has built-in support for deep learning models and includes a ready-to-use Python environment. By creating automated workflows, Amira Software supports scientists with faster image analysis and reproducibility, reducing the learning curve for inexperienced users. Deep learning models accelerate and improve the segmentation and interpretation of complex or large data sets.

Analyze and correlate data

Analyze and correlate data from any imaging modality, at any scale

Amira Software offers native compatibility and expansive correlative analysis to help you better understand your 2D-5D imaging data. It is a flexible software solution that can handle any modality at any scale and size. With a multi-volume infrastructure, Amira Software is designed to perform image registration on as many modalities as desired. It can also perform correlative analysis at either single points in time or as part of longitudinal studies.

Customization

Confidence

Thanks to powerful segmentation and image processing capabilities and workflows, and after 20+ years of collaboration with the scientific community and thousands of researchers, it has been now proven that our digital imaging-based workflows provide reliable answers to biomedical and life science research.

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Support

Thanks to our dedicated professional support team, you get access to our top experts to ensure that no question is left unanswered. And with our training, consulting options, and ever-expanding collection of tutorials and how-to’s, you can reduce your learning curve and focus on getting the answers you are pursuing.

Customization

Customization

Because your needs are unique and keep evolving, our software solutions are fully flexible and open to customization. Thanks to our scripting interface (Python, TCL), bridge with MATLAB, and our programming API, you can expand our software solution and integrate your own IP (Intellectual Property). And, if needed, our professional service team can help you design unique solutions tailored to your needs.


Applications

 

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Techniques

Correlative imaging

With its long-standing applications in multi-modality imaging techniques, Amira Software is the tool of choice for many researchers working with data from different imaging modalities. Amira architecture supports multi-volume data processing and visualization from the ground up. The automatic registration tools integrated into the standard edition of Amira Software with the Multi-Planar Workroom offer the flexibility of the most commonly used automated registration metrics and optimizers that allow for the adjustment of the registration parameters to meet the needs of your data.

 

Membrane detection

Amira Software accelerates segmentation by employing automated detection of cellular features, such as filaments and membranes. By performing advanced image analysis and statistics on the cryo-tomograms, Amira Software combines data from these individual structures, averaging out noise and increasing contrast to create a composite model with higher resolution.

 

Cell detection

Cellular spheroids are 3D cell cultures that represent in vivo tissue better than traditional cellular monolayers, improving the ability of researchers to study cancer, diabetes mellitus, or stem cells among many applications. However, cell analysis in such 3D multicellular objects is not accurately possible, especially without destroying the object of study. Amira Software can automatically separate the cells and perform volumetric, morphometric, and intensity measurements on individual cells and their nuclei in 3D image data of these spheroids. Amira Software also helps researchers with the analysis of conventional 2D cellular monolayers.

 

High Content Screening

Amira Software enables multi-channel quantitivative capabilities to investigate the most demanding scientific and experimental models used in HCS, including immuno-oncology, neuroscience, and organoid health. Thanks to its incredible speed and flexibility, Amira Software helps enable advanced 2D–5D bioimaging workflows in research areas ranging from structural and cellular biology, to neuronal and spheroid morphology in 3D models. To facilitate these advanced analyses, Amira Software features deep learning for improved training and prediction, including "intelligent denoising functionality

Learn more

 

Multi-channel and time-series visualization

With Amira Software’s new Xplore5D extension, life scientists can easily visualize, correlate, and process large multi-channel and time series data in one platform, without worrying about image size or memory limits. With its smart file format, Xplore5D allows you to compress all imaging data without losing precious information collected during acquisition.

Learn more

 

Filament tracing

With Amira Software, you are able to use a template-matching algorithm to automatically detect and trace these fine filaments in noisy cryo-EM or DualBeam data. In addition, Amira Software enables you to reconstruct filamentous networks and edit the resulting graphs to remove image features erroneously identified as filaments or to add missing parts of a network. Graphs of filaments can then be quantified by measuring parameters such as amount, length, thickness, orientation, ranks, etc. Compelling 3D renderings can be created from the reconstructed model and the computed parameters.

 

Correlative imaging

With its long-standing applications in multi-modality imaging techniques, Amira Software is the tool of choice for many researchers working with data from different imaging modalities. Amira architecture supports multi-volume data processing and visualization from the ground up. The automatic registration tools integrated into the standard edition of Amira Software with the Multi-Planar Workroom offer the flexibility of the most commonly used automated registration metrics and optimizers that allow for the adjustment of the registration parameters to meet the needs of your data.

 

Membrane detection

Amira Software accelerates segmentation by employing automated detection of cellular features, such as filaments and membranes. By performing advanced image analysis and statistics on the cryo-tomograms, Amira Software combines data from these individual structures, averaging out noise and increasing contrast to create a composite model with higher resolution.

 

Cell detection

Cellular spheroids are 3D cell cultures that represent in vivo tissue better than traditional cellular monolayers, improving the ability of researchers to study cancer, diabetes mellitus, or stem cells among many applications. However, cell analysis in such 3D multicellular objects is not accurately possible, especially without destroying the object of study. Amira Software can automatically separate the cells and perform volumetric, morphometric, and intensity measurements on individual cells and their nuclei in 3D image data of these spheroids. Amira Software also helps researchers with the analysis of conventional 2D cellular monolayers.

 

High Content Screening

Amira Software enables multi-channel quantitivative capabilities to investigate the most demanding scientific and experimental models used in HCS, including immuno-oncology, neuroscience, and organoid health. Thanks to its incredible speed and flexibility, Amira Software helps enable advanced 2D–5D bioimaging workflows in research areas ranging from structural and cellular biology, to neuronal and spheroid morphology in 3D models. To facilitate these advanced analyses, Amira Software features deep learning for improved training and prediction, including "intelligent denoising functionality

Learn more

 

Multi-channel and time-series visualization

With Amira Software’s new Xplore5D extension, life scientists can easily visualize, correlate, and process large multi-channel and time series data in one platform, without worrying about image size or memory limits. With its smart file format, Xplore5D allows you to compress all imaging data without losing precious information collected during acquisition.

Learn more

 

Filament tracing

With Amira Software, you are able to use a template-matching algorithm to automatically detect and trace these fine filaments in noisy cryo-EM or DualBeam data. In addition, Amira Software enables you to reconstruct filamentous networks and edit the resulting graphs to remove image features erroneously identified as filaments or to add missing parts of a network. Graphs of filaments can then be quantified by measuring parameters such as amount, length, thickness, orientation, ranks, etc. Compelling 3D renderings can be created from the reconstructed model and the computed parameters.

 

Services

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入门培训

通过专门为 Amira、Avizo 和 PerGeos 软件新用户设计的入门培训,缩短学习曲线,使投资收益最大化。

课程包括一个讲座及互动提问环节。培训材料重点讲述 Amira、Avizo 和 PerGeos 软件的基本特点和功能。

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高级培训

通过专为 Amira、Avizo 和 PerGeos 软件的现有用户设计的高级培训使投资收益最大化并缩短取得成果的时间。

课程包括一个讲座及互动提问环节。培训材料重点讲述 Amira、Avizo 和 PerGeos 软件的高级特点和功能。

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定制开发

赛默飞世尔科技在 3D 和图像处理方面拥有超过 25 年的经验,向众多小型和大型机构交付了数百个定制项目,可根据您的特定需求为您提供量身定制的解决方案。

我们可以定制和扩展我们不同级别的软件解决方案。


Testimonials

VetCore, University of Veterinary Medicine uses Amira Software

"Research at Vetmeduni Vienna is quite diverse, covering both clinical and preclinical research areas. We are currently four people working in the imaging facility, providing equipment and supports for researchers in both image acquisition (widefield microscopy, CLSM, spinning disk confocal microscopy, soon also STORM super-resolution microscopy, microscopic X-ray computed tomography) and in data visualization and analysis. Amira Software allows you to build networks, enabling complex interactions between data objects. Biology is also complex, and biological interactions are complex networks. Complex questions require complex tools to address them. In this respect, analysis networks such as used in Amira Software outperform most other software approaches when it comes to complex data analysis. Furthermore, I like that Amira Software is quite open concerning integration of deep learning networks and scripting (Tcl, Matlab, Python,...)."

Stephan Handschuch, PhD
VetCore, University of Veterinary Medicine, Vienna

 

EMBL and DKFZ uses Amira Software

The present testimonial highlights the way Amira Software supported Matthia A. Karreman, MSc, PhD at EMBL and DKFZ, Heidelberg, Germany, in her project on multimodal correlative microscopy to efficiently target single tumor cells in vivo. Read reference paper.
Video: 6 min


Features

导入和处理您的成像数据

    • 处理任何规模、任何大小及任何模态的数据:

    - 生物数据格式
    - 位图格式
    - 显微镜:电子和光学
    - 医学和神经图像格式
    - 分子格式
    - 其他图像采集设备(MRI、放射摄影术等)

    • 有限元建模、几何建模、CAD
    • 支持多数据/多视图、多通道、时间序列、超大数据
    • 缩放、校准、转换、重新采样
    • 图像增强、能满足各种需求的滤波和卷积、傅立叶变换
    • 伪影消除算法
    • 先进的多模式 2D/3D 自动配准
    • 图像对齐、算术运算、相关、融合

    轻松分割成像数据

    • 阈值和自动分割、对象分离、自动标记
    • 区域生长、活动轮廓、插值、卷绕、平滑
    • 形态学处理,包括分水岭和盆地
    • 基于机器学习的分割
    • 自动追踪单个纤维和丝状体
    • 骨架化和纤丝网络提取
    • 交互式工具,用于生成或编辑分割和空间图形
    • 3D 表面重建
    • FEA/CFD 载网生成

     

    导出您的分析和可视化工作以便无缝发布并演示

    • 动画和视频生成
    • 高级关键帧和物体动画
    • 混合图像、几何模型、测量和模拟
    • 注释、测量图例、柱状图和曲线图
    • 导出电子表格、3D 模型和高质量图像
    • 主动和被动 3D 立体视觉
    • 单屏和多屏显示
    • 沉浸式环境

    可视化和探索您的成像数据

    • 交互式高质量体渲染和多通道可视化
    • 正交、倾斜、圆柱形和弧形切面
    • 轮廓绘制和等值面提取
    • 最大信号或其他类型投影
    • 矢量和张量可视化
    • 对象和追踪
    • 分子可视化

    分析成像数据并获得定量信息

    • 直观的模板菜单创建、自定义、自动重放
    • 内置测量项目,包括计数、体积、面积、周长、长径比和方向
    • 用户定义的测量指标
    • 内含电子表格工具和图表的结果查看器
    • 自动单个特征测量、3D 定位和电子表格选择
    • 自动统计、分布图
    • 使用任何测量标准进行特征过滤
    • 数据配准、变形、比较和测量

     

    轻松、快速地调整 Amira 软件以满足您的特定需求

    • 定制 C++ 模块开发
    • MATLAB™ 桥
    • Python 脚本 API

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    Products

    Amira 软件
    生命科学

    • 探索 2D-5D 生物成像数据
    • 识别和理解结构
    • 获取统计信息
    • 分享报告和精彩动画

    Krios G4 Cryo-TEM

    • 改进的人体工程学
    • 可更轻松放进新建或现有的实验室
    • 极大提高生产率和自动化水平
    • 用于高分辨率 3D 重构的最佳成像质量

    Aquilos 2 Cryo-FIB

    • 可自动生成多个薄片
    • 利用提取纳米操纵器锁定并提取感兴趣的结构
    • 用于高分辨率断层扫描的 3D 可视化

    Apreo 2 SEM

    • 高性能 SEM、适用于纳米或纳米以下的所有圆分辨率
    • 用于敏感电视率材料对比度的列内 T1 反向散射检测器
    • 长工作距离 (10 mm) 下性能出色

    Contact us

    For Research Use Only. Not for use in diagnostic procedures.

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