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.
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Particles identification in Nickel-Base Superalloy

Particles identification in Nickel-Base Superalloy

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

FIB Serial Section of Particles in Nickel-Base Superalloy

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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 3 different methods to calculate the tortuosity factor based on on following simulated properties: Absolute Permeability, Molecular Diffusion or Formation Factor

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Average interleaved data

Average interleaved data

Python (pyscro), Project (hx, pgo)

The purpose of this python script object is to average interleaved data.

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View Manager

View Manager

Tcl

This module allows storing and retrieving camera settings for viewer windows to be able to switch easily between different view presets.

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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

Examples showing how to use AI (deep learning models) in an Analyzer recipe (hxisp)

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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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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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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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Convert To Spreadsheet

Convert To Spreadsheet

Python (pyscro)

This module allows the user to convert a scalar/vector/tensor field into a spreadsheet containing the X,Y,Z positions and the values of the field.

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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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DVC Accuracy

DVC Accuracy

Python (pyscro)

This module allows the user to measure the displacement and strain errors from two repeat scans.

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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

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

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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

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

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Auto-Crop script module

Auto-Crop script module

Tcl

Automatically crop your volume data to reduce its size.

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Export Spatial Graph to MS Excel XML document

Export Spatial Graph to MS Excel XML document

Recipe (hxrecipe), Tcl, Demo

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

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Eagleford Shale FIB-SEM Segmentation

Eagleford Shale FIB-SEM Segmentation

Recipe (hxrecipe)

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.

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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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Refine Surface

Refine Surface

XPand module

Module for refining a surface.

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Depthwise Volume Fraction

Depthwise Volume Fraction

Python (pyscro)

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

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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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