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.
NEW
How to Use the Surface View Module and Create Elaborate Surface Renderings
Demo
30 Dec 2021 - This short video demonstrates the basic use of the Surface View module, and how to combine several Surface View modules to create elaborate renderings.
NEW
Tcl
18 Nov 2021 - Module Mask Map By Molecule lets you mask an EM map of a macro molecule by an atomic model of the entire or partial molecule. This can be useful when validating EM maps from SPA with published models from the Protein Data Bank.
NEW
How to Set the Colormap for Ortho Slice and Volume Rendering
Demo
18 Nov 2021 - This tutorial is an introduction to the basic principle and use of colormaps.
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.
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.
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.
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.
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.
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.
How to Edit a Colormap from the Colormap Editor
Demo
14 Sep 2021 - This tutorial demonstrates how to use the Colormap Editor.
Demo
14 Sep 2021 - This short tutorial presents the different options to save a project.
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 - This Xtra contains a 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, and recall metrics for comparing two segmentation labels.
Component Verification Using X-ray Computed Tomography and CAD Comparison
Demo, Data, Misc
3 Mar 2021 - The following video and training material uses an additively manufactured con rod to demonstrate how the surface profile generated from X-ray CT data can be compared to the original component CAD design.
Demo, Misc
24 Feb 2021 - This video tutorial demonstrates how to deal with visualization of large datasets.
Patch Extraction Tools for Deep Learning data preparation
Python (pyscro)
22 Feb 2021 - A set of tools dedicated to the preparation of data for training Deep Learning models and reducing annotation time.
How to Set Up Two-Sided Clipping
Demo
15 Feb 2021 - This tutorial explains how to set up two-sided clipping in order to transition between two visualizations of data.
How to Use Camera Orbit and Animate a Rotation
Demo
15 Feb 2021 - This tutorial explains how to use the Camera Orbit module, and then animate the rotation around an object in the Animation Director.
High Content Screening Plate Manager
Python (pyscro), Tcl
12 Feb 2021 - Load, visualize and process multi-channel fields from Thermo Scientific CellInsight CX5, CX7 LED and CX7 LZR HCA instruments and HCS Studio software.
Demo
10 Feb 2021 - This tutorial explains how to create and export a movie file from the Animation Director.