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.

Green-Lagrange Strain

Green-Lagrange Strain

Python (pyscro)

4 Mar 2020 - This module allows the user to compute the Green-Lagrange strain tensor from a displacement field.

Convert To Volume

Convert To Volume

Python (pyscro)

4 Mar 2020 - This module allows the user to re-map a DVC scalar field (displacement and strain components) stored in a mesh into a lattice dataset (image).

Amira User's Guide translated to Japanese

Amira User's Guide translated to Japanese

Demo, Misc

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

Create Label Annotations

Create Label Annotations

Tcl

13 Dec 2019 - This module creates label annotations from the result of a Label Analysis with the help of the Measurement tool.

Average interleaved data

Average interleaved data

Python (pyscro), Project (hx, pgo)

21 Oct 2019 - The purpose of this python script object is to average interleaved data.

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

Load a Numpy array into PerGeos/Amira-Avizo using the Python API

Load a Numpy array into PerGeos/Amira-Avizo using the Python API

Python (pyscro)

21 Oct 2019 - This script simply reads and loads numpy arrays in a user specified directory into PerGeos/Amira-Avizo as an 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.

Feature segmentation for non-uniform illumination and low-contrast images

Feature segmentation for non-uniform illumination and low-contrast images

Recipe (hxrecipe)

17 Oct 2019 - The recipe lets you segment small features on images with non-uniform illumination and low contrast.

Depthwise Volume Fraction

Depthwise Volume Fraction

Python (pyscro)

17 Oct 2019 - This module allows the user to compute the volume fraction per separated region depending on depth from the surface of a segmented object.

Eagleford Shale FIB-SEM Segmentation

Eagleford Shale FIB-SEM Segmentation

Recipe (hxrecipe)

17 Oct 2019 - This recipe guided workflow will result in a 5-phase segmentation applicable to the included dataset and most typical FIB-SEM data. Input Data, the Recipe, Output data are included here.

Auto-Crop script module

Auto-Crop script module

Tcl

16 Oct 2019 - Automatically crop your volume data to reduce its size.

Simulation-based Tortuosity estimation of porous media

Simulation-based Tortuosity estimation of porous media

Tcl

16 Oct 2019 - Tortuosity is a key factor for material characterization of porous media. This package propose 4 methods to calculate the tortuosity factor based on the xlab properties: Absolute Permeability, Molecular Diffusion, Formation Factor and Thermal Conductivity.

PerGeos TCL script for processing all files in a folder with a recipe

PerGeos TCL script for processing all files in a folder with a recipe

Tcl

16 Oct 2019 - Process all files in a folder by applying the same recipe to all of them individually.

Different methods to measure the volume of fibers generated by XFiber extension

Different methods to measure the volume of fibers generated by XFiber extension

Project (hx, pgo), Demo

16 Oct 2019 - This guideline aims to identify different ways to analyze the volume fraction of fibers traced by the XFiber extension.

Relative pore fraction

Relative pore fraction

Recipe (hxrecipe), Demo, Data

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

Export Spatial Graph to MS Excel XML document

Export Spatial Graph to MS Excel XML document

Recipe (hxrecipe), Tcl, Demo

16 Oct 2019 - An Amira-Avizo recipe to export to a XML document which can be used in MS Excel for further analysis.

Refine Surface

Refine Surface

XPand module

16 Oct 2019 - Module for refining a surface.