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.

NEW Segmentation of agglomerated Ni nanoparticles

Segmentation of agglomerated Ni nanoparticles

Recipe ISP (hxisp,a2d)

24 Aug 2020 - This recipe segments overlapping Ni nanoparticles on a high resolution STEM image after which a size distribution of the nanoparticles can also be computed

NEW Hough Circle Fitting

Hough Circle Fitting

Python (pyscro)

30 Jul 2020 - Generalized Hough transform to fit circles to the image.

NEW Multi-Scale Cylinder Correlation

Multi-Scale Cylinder Correlation

Python (pyscro), Project (hx, pgo)

30 Jul 2020 - This module gives better results for fiber-tracing in the case of multiple fibers with differing or varying diameters in the same dataset.

NEW Segment TEM data without artifact  and background effect

Segment TEM data without artifact and background effect

Recipe (hxrecipe), Tcl, Project (hx, pgo)

10 Jul 2020 - Segment TEM data aided by the Structure enhancement filter.

Disp View

Disp View

Python (pyscro)

4 Mar 2020 - This module allows the user to visualise a vector field, computed using the Digital Volume Correlation module, with arrows coloured according to the magnitude of the vector.

Cumulate Displacement Field

Cumulate Displacement Field

Python (pyscro)

4 Mar 2020 - This module allows the user to add multiple displacement fields.

Green-Lagrange Strain

Green-Lagrange Strain

Python (pyscro)

4 Mar 2020 - This module allows the user to compute the Green-Lagrange strain tensor from a displacement field.

Convert To Volume

Convert To Volume

Python (pyscro)

4 Mar 2020 - This module allows the user to re-map a DVC scalar field (displacement and strain components) stored in a mesh into a lattice dataset (image).

Average interleaved data

Average interleaved data

Python (pyscro), Project (hx, pgo)

21 Oct 2019 - The purpose of this python script object is to average interleaved data.

2D SEM  (White) Grain Segmentation

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

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

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

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

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.

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

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

Recipe (hxrecipe)

17 Oct 2019 - The recipe lets you segment small features on images with non-uniform illumination and low contrast.

Depthwise Volume Fraction

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

Auto-Crop script module

Tcl

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

Simulation-based Tortuosity estimation of porous media

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

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

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

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.