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.

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
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
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.

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

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.

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
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
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.

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.

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