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Avizo930 usersguide Avizo Avizo User ? s Guide CCopyright Information Copyright c - Konrad-Zuse-Zentrum fu ?r Informationstechnik Berlin ZIB Germany Copyright c - FEI SAS All rights reserved Trademark Information Copyright c FEI Amira Avizo and Open Inven

Avizo Avizo User ? s Guide CCopyright Information Copyright c - Konrad-Zuse-Zentrum fu ?r Informationstechnik Berlin ZIB Germany Copyright c - FEI SAS All rights reserved Trademark Information Copyright c FEI Amira Avizo and Open Inventor are trademarks of FEI Company or its af ?liates Visilog and PerGeos are marks of FEI Company or its af ?liates All other trademarks belong to their respective owners Avizo is being jointly developed by Konrad-Zuse-Zentrum fu ?r 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 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 speci ?cations 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 CContents Introduction Overview Features overview Data import Viewing navigation interactivity Visualization of D Image Data Image processing Model reconstruction Visualization of D models and numerical data General Data Processing and Data Analysis Matlab integration High Performance Visualization Automation Customization Extensibility Editions and Extensions Editions Optional Extensions License keywords System Requirements Prioritizing hardware for Avizo How hardware can help optimizing Special considerations C Avizo License Manager Contents About Avizo licensing management License manager actions Licensing troubleshooting Contacting the license administrator First steps in Avizo Contact and Support Getting Started Start the program Loading Data Invoking Editors Visualizing Data Interaction with the Viewer Data Import Tutorials Visualizing and Processing D and D Images How to load image data The Avizo File Browser Reading D Image Data from Multiple D Slices Setting the Bounding Box The Stacked Slices ?le format Working with Large Disk Data Working with out-of-core data ?les LDA Visualizing D Images Orthogonal Slices Simple Data Analysis Resampling the Data Displaying an Isosurface Cropping the Data CONTENTS ii C Volume Rendering Combined D and D views with Ortho Views Avizo Quick start Manage combined D and D views with Ortho Views Intensity Range Partitioning Segmentation of D Images Interactive Image Segmentation Volume and Statistics Measurement Threshold Segmentation Re ?ning Threshold Segmentation Results More Hints about Segmentation Deconvolution for light microscopy General remarks about image deconvolution Data acquisition and sampling rates Standard Deconvolution Tutorial Blind Deconvolution Tutorial Bead Extraction Tutorial Performance issues and multi-processing Tutorials Advanced Image Processing Segmentation and Analysis Getting started with Advanced Image Processing and Quantitative Analysis Processing images Interpretation as D image or D image stack Getting more help Binarization More about binary images More hints about binarization Separation Analysis Interactive selection Filtering based on measures CONTENTS iii C Classifying measures with sieves Label images Processing