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.

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.

Eagleford Shale FIB-SEM Segmentation

Eagleford Shale FIB-SEM Segmentation

Recipe (hxrecipe)

17 Oct 2019 - 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.

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.

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

16 Oct 2019 - Process all files in a folder by applying the same recipe to all of them individually.

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.

Refine Surface

Refine Surface

XPand module

16 Oct 2019 - Module for refining a surface.

View Manager

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

Recipe Sequencer

Recipe (hxrecipe), XPand module, Data

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

Berea Pore Size Distribution Tutorial

Berea Pore Size Distribution Tutorial

Recipe (hxrecipe), Project (hx, pgo), Demo, Data

11 Oct 2019 - Create a semi-automatic workflow for Pore Size Distribution on Berea sandstone

Tutorial: Generate a DVC mesh of complex shapes

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

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

How to use PyQt5 in a pyscro module

Python (pyscro)

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

Convert To Spreadsheet

Convert To Spreadsheet

Python (pyscro)

3 Oct 2019 - 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.

Scalar Extract

Scalar Extract

Python (pyscro)

3 Oct 2019 - This module extracts the displacement and strain components computed using the Digital Volume Correlation module.

Incremental Global DVC

Incremental Global DVC

Python (pyscro)

3 Oct 2019 - 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).

DVC Accuracy

DVC Accuracy

Python (pyscro)

3 Oct 2019 - This module allows the user to measure the displacement and strain errors from two repeat scans.

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

3 Oct 2019 - Examples showing how to use AI (deep learning models) in an Analyzer recipe (hxisp)

Porous Silicon Batch

Porous Silicon Batch

Recipe ISP (hxisp,a2d), Demo, Data

18 Sep 2019 - Batch processing of a subset of porous silicon SEM images.