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 Optical Thin Section Pore Space Characterization in HSV colorspace

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.

NEW XFiber Automation

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.

NEW Molar Segmentation Using Watershed and Top-Hat and Surface Generation

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

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

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

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

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

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

Relative pore fraction

Recipe (hxrecipe), Demo, Data

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

Recipe Sequencer

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

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

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

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

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

Porous Silicon Batch

Recipe ISP (hxisp,a2d), Demo, Data

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

Getting Started with Deep Learning Training

Getting Started with Deep Learning Training

Deep learning model, Data

5 Sep 2019 - Model and companion project for the Deep Learning tutorial.

Three Phase Ti Segmentation

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

Plates in Ti-62222

Plates in Ti-62222

Recipe ISP (hxisp,a2d), Data

24 Jul 2019 - FIB Serial Section of Ti-62222

Particles identification in Nickel-Base Superalloy

Particles identification in Nickel-Base Superalloy

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

24 Jul 2019 - FIB Serial Section of Particles in Nickel-Base Superalloy

Getting Started with Deep Learning Training (Membrane Segmentation)

Getting Started with Deep Learning Training (Membrane Segmentation)

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

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

Size distribution of Nb-Cu nanoparticles

Size distribution of Nb-Cu nanoparticles

Recipe ISP (hxisp,a2d), Demo, Data

26 Jun 2019 - The recipe segments the Nb particles and the Cu particles.