Welcome to the Xtra Library for
Thermo Scientific Amira, Avizo and PerGeos Software
Below you will find a collection of add-ons (recipes, scripts, demos,…) that will help you improve your day-to-day use of Amira-Avizo and PerGeos Software and make you gain both time and efficiency.
Use the Search field to look for specific keywords related to your domain of interest. The different filters also help you target specific resources.
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Incremental Digital Volume Correlation Tutorial
Demo
14 Sep 2021 - This tutorial explains how to use the new features of the Digital Volume Correlation extension to perform a series of incremental measurements.
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How to Use the Image Stack Processing (ISP) Workroom
Demo
14 Sep 2021 - This tutorial demonstrates how to use the ISP workroom, an intuitive 2D workroom for automating image processing workflows in 3D.
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How to Overlay Images Using the Color Wash Module
Demo
14 Sep 2021 - This short video demonstrates how to use the Color Wash module to overlay label colors onto a greyscale image.
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How to Register and Merge Images
Demo
14 Sep 2021 - This short tutorial demonstrates how to use the Register Images and Merge modules to align and merge two images.
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How to Use the Transform Editor
Demo
14 Sep 2021 - This tutorial introduces the concept of geometric transformation in Amira-Avizo and demonstrates data alignment with the Transform Editor.
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How to Create a Custom Label Colormap
Demo
14 Sep 2021 - This short video explains how to create and export a label colormap from the Segmentation Editor.
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How to Change the Label Colormap to Display a Label Field
Demo
14 Sep 2021 - This short video explains how to set an appropriate colormap for label fields with a large number of labels.
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How to Edit a Colormap from the Colormap Editor
Demo
14 Sep 2021 - This tutorial demonstrates how to use the Colormap Editor.
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Demo
14 Sep 2021 - This short tutorial presents the different options to save a project.
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How to Script the Instantiation of a Python Script Object Xtra
Python (pyscro)
9 Sep 2021 - This Xtra provides a script template that can be used to instantiate a Python script object Xtra from the Python console or from a Python script.
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Using Tcl Command Module for Multi-File OBJ Export
Tcl, Project (hx, pgo)
7 Sep 2021 - The Tcl Command Module makes it easy to export the surfaces of single objects from a multi-object surface as OBJ (Wavefront) files.
Data
8 Jul 2021 - This Xtra provides the data used in the tutorials for the Xplore5D extension, available in Amira-Avizo 2021.1
XPand module
29 Jun 2021 - The Split and Merge Segments module merges the two most representative segments at the intersection points of a graph structure and detaches the others.
More Resources on Amira-Avizo Learning Center YouTube Playlist
Demo, Misc
4 Jun 2021 - This Xtra provides links to Amira-Avizo Learning Center YouTube playlist.
Browse TensorBoard of old Deep Learning Training sessions
Deep learning model, Python (pyscro)
21 May 2021 - This Xtra proposes a module allowing you to browse TensorBoard logs from previous Deep Learning Training sessions.
Python (pyscro)
29 Mar 2021 - AddDataToPointCloud writes data defined on mesh-nodes into a point-cloud with equal number of points. Together with the Xtra "PointCloudToSpreadsheet", the module can e.g. be used to export the results created by the module Surface Distance.
Python (pyscro), Project (hx, pgo)
29 Mar 2021 - The Extract Oriented Labels module extracts every label from the input label image, and resamples each image along its own main orientations (or eigenvectors).
Tcl
8 Mar 2021 - Script module to fit molecular models to density maps, a process frequently called "docking".
Image Segmentation Evaluation Using Standard Metrics (Python)
Python (pyscro), Project (hx, pgo)
8 Mar 2021 - Segmentation evaluation using standard precision, recall metrics for comparing two segmentation labels.
Getting Started with Flatten Module
Project (hx, pgo), Demo
8 Mar 2021 - This tutorial demonstrates use of the Flatten experimental module to create interactive contours by defining the unfolding surface while respecting the constraints of the module inputs.
Demo, Misc
24 Feb 2021 - This video tutorial demonstrates how to deal with visualization of large datasets.