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.

Getting Started with Flatten module NEW
Add-on How-to

Getting Started with Flatten module

Project (hx, pgo), Demo

8 Mar 2021 - Get started with the Flatten experimental module. You will learn how to create interactive contours by defining the unfolding surface while respecting the constraints of the module inputs. The contours will be manually defined on the chocolate-bar.am.

Component Verification Using X-ray Computed Tomography and CAD Comparison NEW
How-to

Component Verification Using X-ray Computed Tomography and CAD Comparison

Demo, Data, Misc

3 Mar 2021 - The following video and training material will use 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.

Large Data Visualization NEW
Add-on How-to

Large Data Visualization

Demo, Misc

24 Feb 2021 - This video tutorial demonstrates how to deal with visualization of large datasets.

How to Set Up Two-Sided Clipping NEW
How-to

How to Set Up Two-Sided Clipping

Demo

15 Feb 2021 - This short tutorial explains how to set up two-sided clipping in order to transition between two visualization of data.

How to Use Camera Orbit and Animate a Rotation NEW
How-to

How to Use Camera Orbit and Animate a Rotation

Demo

15 Feb 2021 - This short tutorial explains how to use the Camera Orbit module and then animate the rotation around an object in the Animation Director.

How to Create a Movie File NEW
How-to

How to Create a Movie File

Demo

10 Feb 2021 - This tutorial explains how to export a movie file from the Animation Director.

How to Compare Slices Side by Side NEW
How-to

How to Compare Slices Side by Side

Demo

10 Feb 2021 - This short tutorial explains how to compare side by side two slices displaying different information, for example of raw data and its corresponding labeled image.

Non-Standard Python Package Installation Tutorial
How-to

Non-Standard Python Package Installation Tutorial

Demo, Misc

13 Jan 2021 - Brief video explaining how to install a Python package in a newly created Python environment using pip or edm.

Multi-Component Analysis of X-ray Computed Tomography Datasets
Add-on How-to

Multi-Component Analysis of X-ray Computed Tomography Datasets

Recipe (hxrecipe), Project (hx, pgo), Demo, Data, Misc

4 Jan 2021 - The following videos and training material detail the steps taken to automate the analysis of multiple parts in a single X-ray CT volume.

Analysis of X-ray CT Calibration Spheres Using the Metrology Workroom
How-to

Analysis of X-ray CT Calibration Spheres Using the Metrology Workroom

Demo, Data, Misc

4 Jan 2021 - This video presents how to use the Metrology workroom to analyze calibration spheres used in X-ray Computed Tomography.

How to Create and Animate a Camera Path
How-to

How to Create and Animate a Camera Path

Demo

3 Jan 2021 - This short tutorial explains how to create a camera path and then animate the camera along this path with the Animation Director.

How to Animate the Appearance of Objects with the Animation Director
How-to

How to Animate the Appearance of Objects with the Animation Director

Demo

3 Jan 2021 - This short tutorial explains how to animate the appearance and disappearance of objects with the Animation Director.

How to Get Started with the Animation Director
How-to

How to Get Started with the Animation Director

Demo

3 Jan 2021 - This short tutorial will take you through the basis of animation creation with the Animation Director.

AMIRA_LOCAL Setup Tutorial
How-to

AMIRA_LOCAL Setup Tutorial

Demo

5 Oct 2020 - Brief video explaining how to set up an AMIRA_LOCAL path on Windows 10.

2D Cell Tracking Example
Add-on

2D Cell Tracking Example

Recipe (hxrecipe), Project (hx, pgo), Demo, Data

24 Aug 2020 - A 2D cell tracking example from a multichannel time series data set. Contains a segmentation recipe, modules needed to track the cells through time, and a video of the finished result.

Cell Detection and Tracking 2020.2
Add-on How-to

Cell Detection and Tracking 2020.2

Recipe ISP (hxisp,a2d), Python (pyscro), Project (hx, pgo), Demo

21 Aug 2020 - Simple workflow for tracking cell nuclei in a 3D Time Series.

Create a porosity analysis recipe
How-to

Create a porosity analysis recipe

Recipe (hxrecipe), Demo

15 Jul 2020 - This tutorial explains how to create a simple porosity analysis and turn it into a push-button recipe.

Avizo User's Guide translated to Japanese
Add-on How-to

Avizo User's Guide translated to Japanese

Demo, Misc

11 May 2020 - You will find here a selection of Avizo tutorials translated to Japanese.

Molar Segmentation Using Watershed and Top-Hat and Surface Generation
Add-on How-to

Molar Segmentation Using Watershed and Top-Hat and Surface Generation

Project (hx, pgo), Demo, Data

11 May 2020 - Data, tutorial, and complete project for segmenting a CT-scanned human molar artifact. The tutorial and project cover advanced image segmentation and surface generation.

Amira User's Guide translated to Japanese
Add-on How-to

Amira User's Guide translated to Japanese

Demo, Misc

29 Jan 2020 - You will find here a large selection of Amira tutorials translated to Japanese.

Length Distribution Analysis
Add-on How-to

Length Distribution Analysis

Recipe (hxrecipe), Project (hx, pgo), Demo, Data

21 Oct 2019 - This tutorial demonstrated how to quantify thickness distribution along the length