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.
Python (pyscro)
4 Mar 2020 - This module allows the user to compute the Green-Lagrange strain tensor from a displacement field.
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
Demo, Misc
29 Jan 2020 - You will find here a selection of Amira tutorials translated to Japanese.
Tcl
13 Dec 2019 - This module creates label annotations from the result of a Label Analysis with the help of the Measurement tool.
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
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.
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
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.
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
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.
Tcl
16 Oct 2019 - Automatically crop your volume data to reduce its size.
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.
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
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.
