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.

Relative Area Fraction for Amira-Avizo2D
Add-on How-to

Relative Area Fraction for Amira-Avizo2D

Recipe ISP (hxisp,a2d), Python (pyscro), Data, Misc

5 Oct 2020 - This Xtra provides a module to help compute the area fraction of a label over the area of another label in Amira-Avizo2D.

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.

Optical Thin Section Pore Space Characterization in HSV colorspace
Add-on

Optical Thin Section Pore Space Characterization in HSV colorspace

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

10 Jul 2020 - Optical Thin Section Pore Space is segmented converting RGBA images in HSV colorspace via Python scripts.

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

Random Forests for Multiclass Segmentation using Python API in PerGeos
Add-on

Random Forests for Multiclass Segmentation using Python API in PerGeos

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

21 Oct 2019 - Simple demonstration of feature computation where the feature vector contains intensity and 2D eigenvalues (X & Y). This example uses random forests implementation from the sklearn package.

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.

Berea Pore Size Distribution Tutorial
Add-on How-to

Berea Pore Size Distribution Tutorial

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

11 Oct 2019 - Create a semi-automatic workflow for Pore Size Distribution on Berea sandstone

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)

Porous Silicon Batch
Add-on

Porous Silicon Batch

Recipe ISP (hxisp,a2d), Data

18 Sep 2019 - Batch processing of a subset of porous silicon SEM images.

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

Getting Started with Deep Learning Training for Image Segmentation

Deep learning model, Data

5 Sep 2019 - This is a model and companion project for the Deep Learning tutorial.

Three Phase Ti Segmentation
Add-on

Three Phase Ti Segmentation

Recipe ISP (hxisp,a2d), Data

24 Jul 2019 - Alpha, Borides, Beta segmentation of FIB Serial Section Dataset of Ti Alloy with Borides