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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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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Automated sizing of large area nanoparticles

Automated sizing of large area nanoparticles

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

The recipe segments large area Pt-Rh nanoparticles at high resolution (TEM image).

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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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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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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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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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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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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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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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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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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

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.

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