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.

BSE SEM denoiser

BSE SEM denoiser

Deep learning model

U-Net model for denoising back-scattered SEM images.

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How to use PyQt5 in a pyscro module

How to use PyQt5 in a pyscro module

Python (pyscro)

This example shows how to use PyQt5 in a pyscro module.

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Parameter optimization for auto-thresholding a data

Parameter optimization for auto-thresholding a data

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

In this pyscro example we use opencv and matplotlib to automatically calculate an optimized parameter for thresholding the data based on various metrics.

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Porosity in a battery separator

Porosity in a battery separator

Recipe ISP (hxisp,a2d), Demo, Data

The recipe classifies the pores in a battery separator (SEM image).

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Porosity in a polymer divider

Porosity in a polymer divider

Recipe ISP (hxisp,a2d), Demo, Data

The recipe detects pores in a polymer divider (SEM image).

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Au-Ni-Cl Nanoparticles

Au-Ni-Cl Nanoparticles

Recipe ISP (hxisp,a2d)

This recipe segments nanoparticles of different element from an EDS map.

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Additive Manufacturing Powder

Additive Manufacturing Powder

Recipe ISP (hxisp,a2d)

Segmentation of the particles located in the foreground of the SEM image.

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Amira User's Guide translated to Japanese

Amira User's Guide translated to Japanese

Demo, Misc

You will find here a selection of Amira tutorials translated to Japanese.

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

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

Recipe (hxrecipe)

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

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Simulation-based Tortuosity estimation of porous media

Simulation-based Tortuosity estimation of porous media

Tcl

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.

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Porosity Clustering Analysis and Distance to Surface

Porosity Clustering Analysis and Distance to Surface

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

This tutorial demonstrates the steps to quantify porosity distribution and the distance to surface analysis.

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Tutorial: Generate a DVC mesh of complex shapes

Tutorial: Generate a DVC mesh of complex shapes

Demo, Data

This tutorial described how to build a DVC mesh for specimens with complex shapes.

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Scalar Extract

Scalar Extract

Python (pyscro)

This module extracts the displacement and strain components computed using the Digital Volume Correlation module.

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Relative pore fraction

Relative pore fraction

Recipe (hxrecipe), Demo, Data

The calculation of a relative pore fraction for each separated grains.

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Refine Surface

Refine Surface

XPand module

Module for refining a surface.

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Recipe Sequencer

Recipe Sequencer

Recipe (hxrecipe), XPand module, Data

Module for sequencing a recipe on each individual isolated label from a label field.

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Plates in Ti-62222

Plates in Ti-62222

Recipe ISP (hxisp,a2d), Data

FIB Serial Section of Ti-62222

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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)

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

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Length Distribution Analysis

Length Distribution Analysis

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

This tutorial demonstrated how to quantify thickness distribution along the length

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Incremental Global DVC

Incremental Global DVC

Python (pyscro)

Perform incremental DVC analysis for a series of deformed image, using either small strain or large strain approaches (note: to run correctly the Green Lagrange strain script needs to be installed).

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