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.

Copy Measure Annotation Settings
Add-on

Copy Measure Annotation Settings

Tcl

15 Apr 2020 - This Tcl script-object can be used to copy visualisation settings from one measure to all others in a Measurement module. It is also possible to save/load settings to/from a text file.

Caption From Port
Add-on

Caption From Port

Tcl

15 Apr 2020 - Use this module to fill the text field of a Caption module with the value of a port of another module.

Scale-Space Laplacian of Gaussian Filter
Add-on

Scale-Space Laplacian of Gaussian Filter

Python (pyscro)

15 Apr 2020 - Image processing filter enhancing spherical or blob like objects of various sizes.

Create Label Annotations
Add-on

Create Label Annotations

Tcl

13 Dec 2019 - This module creates label annotations from the result of a Label Analysis with the help of the Measurement tool.

2D SEM  (White) Grain Segmentation
Add-on

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
Add-on

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.

Length Distribution Analysis
Add-on How-to

Length Distribution Analysis

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
Add-on How-to

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
Add-on

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.

Depthwise Volume Fraction
Add-on

Depthwise Volume Fraction

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.

Auto-Crop script module
Add-on

Auto-Crop script module

Tcl

16 Oct 2019 - Automatically crop your volume data to reduce its size.

Simulation-based Tortuosity estimation of porous media
Add-on

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.

Different methods to measure the volume of fibers generated by XFiber extension
Add-on How-to

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.

Relative pore fraction
Add-on How-to

Relative pore fraction

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
Add-on How-to

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.

Refine Surface
Add-on

Refine Surface

XPand module

16 Oct 2019 - Module for refining a surface.

View Manager
Add-on

View Manager

Tcl

14 Oct 2019 - This module allows storing and retrieving camera settings for viewer windows to be able to switch easily between different view presets.

Recipe Sequencer
Add-on

Recipe Sequencer

Recipe (hxrecipe), XPand module, Data

14 Oct 2019 - Module for sequencing a recipe on each individual isolated label from a label field.

Tutorial: Generate a DVC mesh of complex shapes
Add-on How-to

Tutorial: Generate a DVC mesh of complex shapes

Demo, Data

10 Oct 2019 - This tutorial describes how to build a DVC mesh for specimens with complex shapes.

Parameter optimization for auto-thresholding a data
Add-on

Parameter optimization for auto-thresholding a data

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

7 Oct 2019 - In this pyscro example we use opencv and matplotlib to automatically calculate an optimized parameter for thresholding the data based on various metrics.

How to use PyQt5 in a pyscro module
Add-on

How to use PyQt5 in a pyscro module

Python (pyscro)

7 Oct 2019 - This example shows how to use PyQt5 in a pyscro module.