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Avizo 9 Avizo User’s Guide Copyright Information Copyright (c) 1995-2016 Konra

Avizo 9 Avizo User’s Guide Copyright Information Copyright (c) 1995-2016 Konrad-Zuse-Zentrum f¨ ur Informationstechnik Berlin (ZIB), Germany Copyright (c) 1999-2016 FEI, SAS All rights reserved. Trademark Information: Copyright (c) 2016, FEI. Amira, Avizo, and Open Inventor are trademarks of FEI Company or its afﬁliates. Visilog and PerGeos are marks of FEI Company or its afﬁliates. All other trademarks belong to their respective owners. Avizo is being jointly developed by Konrad-Zuse-Zentrum f¨ ur Informationstechnik Berlin (ZIB) and FEI, SAS. The Avizo XEarth Extension and the Avizo XLVolume Extension include user protection under license for Landmark U.S. Patent Numbers 6,765,570. This manual has been prepared for FEI licensees solely for use in connection with software supplied by FEI and is furnished under a written license agreement. This material may not be used, reproduced or disclosed, in whole or in part, except as permitted in the license agreement or by prior written authorization of FEI. Users are cautioned that FEI reserves the right to make changes without notice to the speciﬁcations and materials contained herein and shall not be responsible for any damages (including consequential) caused by reliance on the materials presented, including but not limited to typographical, arithmetic or listing errors. Contents 1 Introduction 1 1.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 1.2 Features overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 1.2.1 Data import . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 1.2.2 Viewing, navigation, interactivity . . . . . . . . . . . . . . . . . . . . . . . . 3 1.2.3 Visualization of 3D Image Data . . . . . . . . . . . . . . . . . . . . . . . . . 3 1.2.4 Image processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 1.2.5 Model reconstruction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1.2.6 Visualization of 3D models and numerical data . . . . . . . . . . . . . . . . . 6 1.2.7 General Data Processing and Data Analysis . . . . . . . . . . . . . . . . . . 7 1.2.8 Matlab integration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 1.2.9 High Performance Visualization . . . . . . . . . . . . . . . . . . . . . . . . 8 1.2.10 Automation, Customization, Extensibility . . . . . . . . . . . . . . . . . . . 8 1.3 Editions and Extensions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 1.3.1 Editions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 1.3.2 Optional Extensions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 1.3.3 License keywords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 1.4 System Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 1.4.1 Prioritizing hardware for Avizo . . . . . . . . . . . . . . . . . . . . . . . . . 13 1.4.2 How hardware can help optimizing . . . . . . . . . . . . . . . . . . . . . . . 17 1.4.3 Special considerations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 1.5 Avizo License Manager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 1.5.1 Contents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 1.5.2 About Avizo licensing management . . . . . . . . . . . . . . . . . . . . . . . 22 1.5.3 License manager actions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 1.5.4 Licensing troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 1.5.5 Contacting the license administrator . . . . . . . . . . . . . . . . . . . . . . 44 1.6 First steps in Avizo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44 1.7 Contact and Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 2 Getting Started 49 2.1 Start the program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49 2.2 Loading Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 2.3 Invoking Editors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53 2.4 Visualizing Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53 2.5 Interaction with the Viewer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54 2.6 Data Import . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 3 Tutorials: Visualizing and Processing 2D and 3D Images 59 3.1 How to load image data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59 3.1.1 The Avizo File Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60 3.1.2 Reading uploads/Marketing/ avizo930-usersguide.pdf