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Images can aid in understanding cell structure and mechanisms.
As a cell biologist, you know how important it is to understand the intricate mechanisms of cell structure and function. However, analyzing data from various imaging systems and modalities that use different file formats can be a daunting task. Each experimental setup presents a unique challenge, and multi-scale dynamic processes require the tracking of objects of various sizes, from diffraction-limited particles to entire cells. With data sets containing anywhere from a few dozen to tens of thousands of objects, identifying and quantifying sub-cellular structures that support intracellular processes can seem overwhelming.
Thermo Scientific Amira Software is a powerful toolbox that enables cell biologists to visualize, process, and analyze complex biological data in 3D. With its advanced image processing, visualization, and analysis tools, Amira software can help you gain insights into the structure and function of cells and tissues that would be impossible to see with 2D images alone.
Whether you're studying cellular processes, tissue organization, or the effects of drugs on cells, Amira software can help you gain a deeper understanding of your images. With our easy-to-use interface and comprehensive tools, you can streamline your workflow and spend more time doing what you do best - advancing the field of cell biology.
Imaging data
Processing
Visualization
Analysis
信頼性
当社のデジタルイメージングベースのワークフローは、パワフルなセグメンテーションや画像処理能力およびワークフローを備えており、また科学コミュニティや数千人もの研究者との20年以上にわたるコラボレーション実績があるため、生物医学およびライフサイエンスの研究において信頼できる答えを提供することが実証されています。
カスタマイズ
お客様のニーズはそれぞれ異なり、常に進化しているため、当社のソフトウェアソリューションは非常に柔軟で、自由にカスタマイズできます。当社のスクリプトインターフェース（Python、TCL）、MATLABとのブリッジ、およびプログラミングAPIを利用することにより、当社のソフトウェアソリューションを拡張し、お客様独自のIP（知的財産）を統合できます。また必要に応じて、当社のプロフェッショナルサービスチームがお客様のニーズに合わせた独自ソリューションの設計をお手伝いします。
サポート
当社は専用のプロフェッショナルサポートチームを配備しているため、トップエキスパートに問い合わせて、あらゆる質問に対する回答を得ることができます。また、当社のトレーニングやコンサルティングオプション、拡張し続けているチュートリアルやハウ・ツーを活用することで学習時間を短縮し、追求している答えを見つけることに集中できます。
自動化
自動化機能や拡大を続けるアドオンのオンラインレポジトリ（Xtra Gallery）により、繰り返し可能なワークフローを再現が容易なレシピに変換きます。人工知能が追加されているため、画像処理専門家以外でも分析が可能で、複雑な分析に費やす時間を短縮しながら結果の一貫性を維持できます。
Introduction to Amira Software for cell biology
During this 20-minutes webinar, you will learn how to:
- Accelerate subcellular (membrane, organelle) detection and segmentation from Electron Microscopy (TEM) data using a range of readily available tools, including 3D Deep Learning model training.
- Analyze multichannel fluorescence endothelial cell culture data by performing fast and effective cleaning, segmentation, volume colocalization and neighbor cell proximity.
- Extract complex information in 3D such as detection, segmentation and penetration of cancer or immune cells to manage multichannel High Content Screening multi-well images of organoid models.
- Quickly convert, visualize and accurately process large (~100GB) multi-channel and time series light sheet tissue imaging data.
Use cases and insight from your peers
Explore industry-leading insights and research that can support your lab workflow.
Helping scientists answer questions that enable breakthrough discoveries in life sciences, materials science, and industry.
 | Correlative Microscopy: Using Amira Software to Understand the Spread of Cancer Read more |
 | Amira Software Accelerates Veterinary Research with 3D Visualization and Analysis Read more |
 | Molecular Clarity—Discovering What’s Possible with Cryo-Electron Tomography Read more |
 | Cryo-Electron Tomography and 3D Software Advances Coronavirus Research Read more |
Understanding the complexity of cancer with correlative light electron microscopy and Amira Software
Investigating the role of MCI in Alzheimer’s disease with Volumescope SEM and Amira Software
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 with the analysis of conventional 2D cellular monolayers.
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 Software’s 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.
Multi-channel and time-series visualization
With our new Xplore5D extension for Amira Software, life scientists can easily visualize, correlate, and process large multichannel 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.
High-content screening
Amira Software enables multi-channel quantitative 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.
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 instrument 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.
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 with the analysis of conventional 2D cellular monolayers.
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 Software’s 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.
Multi-channel and time-series visualization
With our new Xplore5D extension for Amira Software, life scientists can easily visualize, correlate, and process large multichannel 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.
High-content screening
Amira Software enables multi-channel quantitative 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.
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 instrument 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.
初級者向けトレーニング
Amira、Avizo、およびPerGeosソフトウェアの新規ユーザー用に設計された初級者向けトレーニングは学習速度を高め、投資を最大化します。
このコースは講義と実践セッションで構成されています。トレーニング教材は、Amira、Avizo、およびPerGeosソフトウェアの基本的な特長や機能を取り上げています。
上級者向けトレーニング
Amira、Avizo、およびPerGeosソフトウェアの既存ユーザー用に設計された上級者向けトレーニングは投資を最大化し、結果までの時間の短縮します。
このコースは講義と実践セッションで構成されています。トレーニング教材は、Amira、Avizo、およびPerGeosソフトウェアの高度な特長や機能を取り上げています。
カスタム開発
サーモフィッシャーサイエンティフィックには25年以上にわたる3Dおよび画像処理の経験と、大小の規模の組織に提供してきたカスタムプロジェクトの実績があり、お客様の独自のニーズに合わせてソリューションを提供できます。
当社のソフトウェアソリューションをさまざまなレベルでカスタマイズおよび拡張できます。
Dr. Antentor Hinton Jr, has made extensive use of Amira Software as part of his lab’s work in mitochondrial research.
Amira Software is crucial for visualizing SBF-SEM (serial block-face SEM) and FIB-SEM images, so we can analyze the 3D morphology of organelles.
Dr. Antentor Hinton Jr
Department of Molecular Physiology and Biophysics, Vanderbilt University
Matthia A. Karreman at EMBL and DKFZ, Heidelberg, Germany, uses Amira Software
This 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.
Matthia A. Karreman, MSc, PhD
EMBL and DKFZ, Heidelberg, Germany
"Amira Software helps to set up complex data processing workflows. The first aim was to enhance the contrast of viral and cellular membranes. We applied a combination of 3D non-local means filter and the Membrane Enhancement Filter implemented in Amira Software. An initial automated segmentation was achieved using the Top-hat segmentation tool. This initial segmentation was further manually refined utilizing a Wacom graphics tablet. Based on the refined membrane segmentation, a 3D surface was calculated using unconstrained smoothing, and the surface was visualized as 3D model."
By Steffen Klein (Chlanda lab, Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany)
Amira software solution for the analysis of time series data of cellular processes.
Amira Software can automatically count the cell nuclei which correspond to the cell count of the 3D spheroid cell cultures.
With incredible speed and flexibility, Amira Software enables advanced 2D-5D bioimaging workflows in research areas ranging from structural and cellular biology, to spheroid or tumor analysis and tissue imaging.
Golgi apparatus of green alga Chlamydomonas reihardtii, flas-frozen without any artificial staining or fixatives, and thinned by cryo-FIB milling.
SARS-CoV-2 virion budding and assembly at the ERGIC membrane. A 3D volume rendering is shown for each area with cellular and viral membranes in green and magenta respectively, viral spike proteins in yellow, and viral ribonucleoproteins in cyan.
Amira Software provides a comprehensive toolset for the flexible and accurate analysis of time series data of cellular processes.
Amira software solution for the analysis of time series data of cellular processes.
Amira Software can automatically count the cell nuclei which correspond to the cell count of the 3D spheroid cell cultures.
With incredible speed and flexibility, Amira Software enables advanced 2D-5D bioimaging workflows in research areas ranging from structural and cellular biology, to spheroid or tumor analysis and tissue imaging.
Golgi apparatus of green alga Chlamydomonas reihardtii, flas-frozen without any artificial staining or fixatives, and thinned by cryo-FIB milling.
SARS-CoV-2 virion budding and assembly at the ERGIC membrane. A 3D volume rendering is shown for each area with cellular and viral membranes in green and magenta respectively, viral spike proteins in yellow, and viral ribonucleoproteins in cyan.
Amira Software provides a comprehensive toolset for the flexible and accurate analysis of time series data of cellular processes.
画像データのインポートおよび処理
- あらゆる規模、あらゆるサイズのモダリティを処理
- バイオフォーマット
- ビットマップフォーマット
- 顕微鏡：電子および光学
- 医学および神経画像フォーマット
- 分子フォーマット
- その他の画像取得機器（MRI、X線など）
- 有限要素モデリング、幾何モデリング、CAD
- マルチデータ／マルチビュー、マルチチャンネル、時系列、非常に大きなデータのサポート
- 倍率、校正、変換、試料の再採取
- 画像補正、広範囲フィルタリングおよび畳み込み、周波数フーリエ変換
- アーティファクト低減アルゴリズム
- 高度なマルチモード2D／3D自動登録
- 画像スタックアライメント、演算、相関、統合
画像データの容易なセグメンテーション
- 閾値化および自動セグメンテーション、物体の分離、自動ラベリング
- 領域拡張法、スネーク法、内挿、ラッピング、平滑化
- Watershedアルゴリズムやbasinアルゴリズムなどの形態学的処理
- 機械学習に基づくセグメンテーション
- 個々の繊維、フィラメントの自動トレース
- 細線化およびフィラメントネットワーク抽出
- セグメンテーションまたは空間グラフの生成と編集のためのインタラクティブツール
- 3D表面再構成
- FEA／CFD のグリッド生成
分析および視覚化の成果をエクスポートしてシームレスに公開および発表
- アニメーションおよび動画の作成
- 高度なキーフレームとオブジェクトアニメーション
- 画像、幾何学的モデル、測定値、シミュレーションをミックス
- 注釈、測定の凡例、ヒストグラム、曲線プロット
- スプレッドシート、3Dモデル、高品質の画像をエクスポート
- 能動的および受動的3次元ステレオビジョン
- 単一またはタイルドスクリーンディスプレイ
- 没入環境
画像データの可視化と探索
- インタラクティブな高品質ボリュームおよびマルチチャンネルの可視化
- 直角、傾斜、円柱状、曲線状の切断
- 輪郭およびアイソサーフェス抽出
- 最大値投影法または他の種類の投影法
- ベクトルおよびテンソルの可視化
- 物体および追跡
- 分子可視化
画像データの解析と定量情報の取得
- 直感的なレシピの作成、カスタマイズ、自動再実行
- カウント、容積、面積、周囲長、アスペクト比、方向などの測定機能を搭載
- ユーザー定義の方法
- スプレッドシートツールおよび図表による結果表示
- 個々の機能の自動測定、3Dローカリゼーション、スプレッドシート選択
- 自動統計、分布図
- 任意の測定基準を使用した特徴フィルタリング
- データ登録、変形、比較および測定
ユーザーニーズに合わせた、Amiraソフトウェアの容易かつ迅速な適応
- カスタムC++モジュールの開発
- MATLAB™ブリッジ
- PythonスクリプトAPI
For Research Use Only. Not for use in diagnostic procedures.
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