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

2D SEM (White) Grain Segmentation

Recipe (hxrecipe), Data

This recipe segments and calculate the physical attributes of the white grains in the 2D SEM image

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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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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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Auto-Crop script module

Auto-Crop script module

Tcl

Automatically crop your volume data to reduce its size.

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Create Label Annotations

Create Label Annotations

Tcl

This module creates label annotations from the result of a Label Analysis with the help of the Measurement tool.

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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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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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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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Refine Surface

Refine Surface

XPand module

Module for refining a surface.

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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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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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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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Particle agglomeration

Particle agglomeration

Recipe ISP (hxisp,a2d), Demo, Data

The recipe segments particles that are touching each other, and individual ones.

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Porous silicon

Porous silicon

Recipe ISP (hxisp,a2d), Demo, Data

The recipe detects pores in a porous silicon.

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Size distribution of Nb-Cu nanoparticles

Size distribution of Nb-Cu nanoparticles

Recipe ISP (hxisp,a2d), Demo, Data

The recipe segments the Nb particles and the Cu particles.

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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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Three Phase Ti Segmentation

Three Phase Ti Segmentation

Recipe ISP (hxisp,a2d), Data

Alpha, Borides, Beta segmentation of FIB Serial Section Dataset of Ti Alloy with Borides

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Porous Silicon Batch

Porous Silicon Batch

Recipe ISP (hxisp,a2d), Demo, Data

Batch processing of a subset of porous silicon SEM images.

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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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