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.

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.

Thresholding From Mean
Add-on How-to

Thresholding From Mean

Python (pyscro), Data

4 Jan 2021 - This module performs an adaptive global thresholding of the input image by computing a deviation from the mean of its grayscale values.

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.

XFiber Automation
Add-on

XFiber Automation

Tcl, Project (hx, pgo), Data

17 Jun 2020 - To make use of XFiber, the user usually needs to input many parameters. This package provides 2 tools to ease Xfiber process by presetting Cylinder Correlation and Auto Trace Correlation modules values.

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.

2D SEM  (White) Grain Segmentation
Add-on

2D SEM (White) Grain Segmentation

Recipe (hxrecipe), Data

21 Oct 2019 - This recipe segments and calculate the physical attributes of the white grains in the 2D SEM image

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

Porosity Clustering Analysis and Distance to Surface
Add-on How-to

Porosity Clustering Analysis and Distance to Surface

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

21 Oct 2019 - This tutorial demonstrates the steps to quantify porosity distribution and the distance to surface analysis.

Cracks and cavities segmentation in CT data
Add-on

Cracks and cavities segmentation in CT data

Recipe (hxrecipe), Data

21 Oct 2019 - This recipe is useful in segmenting data with cracks/pores and cavities.

Relative pore fraction
Add-on How-to

Relative pore fraction

Recipe (hxrecipe), Demo, Data

16 Oct 2019 - The calculation of a relative pore fraction for each separated grains.

Recipe Sequencer
Add-on

Recipe Sequencer

Recipe (hxrecipe), XPand module, Data

14 Oct 2019 - Module for sequencing a recipe on each individual isolated label from a label field.

Tutorial: Generate a DVC mesh of complex shapes
Add-on How-to

Tutorial: Generate a DVC mesh of complex shapes

Demo, Data

10 Oct 2019 - This tutorial describes how to build a DVC mesh for specimens with complex shapes.

Parameter optimization for auto-thresholding a data
Add-on

Parameter optimization for auto-thresholding a data

Python (pyscro), Project (hx, pgo), Data

7 Oct 2019 - In this pyscro example we use opencv and matplotlib to automatically calculate an optimized parameter for thresholding the data based on various metrics.

How to use deep learning models in AmiraAvizo2D Analyzer
Add-on

How to use deep learning models in AmiraAvizo2D Analyzer

Recipe ISP (hxisp,a2d), Deep learning model, Data

3 Oct 2019 - Examples showing how to use AI (deep learning models) in an Analyzer recipe (hxisp)

Plates in Ti-62222
Add-on

Plates in Ti-62222

Recipe ISP (hxisp,a2d), Data

24 Jul 2019 - FIB Serial Section of Ti-62222

Getting Started with Deep Learning Training for Image Segmentation
Add-on

Getting Started with Deep Learning Training for Image Segmentation

Deep learning model, Project (hx, pgo), Data

27 Jun 2019 - Model and companion project for the Deep Learning tutorial.

Porosity in a Battery Separator
Add-on

Porosity in a Battery Separator

Recipe ISP (hxisp,a2d), Data

26 Jun 2019 - The recipe classifies the pores in a battery separator (SEM image).

Porosity in a Polymer Divider
Add-on

Porosity in a Polymer Divider

Recipe ISP (hxisp,a2d), Demo, Data

26 Jun 2019 - The recipe detects pores in a polymer divider (SEM image).