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 AMIRA_LOCAL Setup Tutorial

AMIRA_LOCAL Setup Tutorial

Demo, Video

5 Oct 2020 - Brief video explaining how to set up an AMIRA_LOCAL path on Windows 10.

NEW 2D Cell Tracking Example

2D Cell Tracking Example

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

24 Aug 2020 - A 2D cell tracking example from a multichannel time series data set. Contains a segmentation recipe, modules needed to track the cells through time, and a video of the finished result.

NEW Cell Detection and Tracking 2020.2

Cell Detection and Tracking 2020.2

Recipe ISP (hxisp,a2d), Python (pyscro), Project (hx, pgo), Demo

21 Aug 2020 - Simple workflow for tracking cell nuclei in a 3D Time Series.

Create a porosity analysis recipe

Create a porosity analysis recipe

Recipe (hxrecipe), Demo

15 Jul 2020 - This tutorial explains how to create a simple porosity analysis and turn it into a push-button recipe.

Avizo User's Guide translated to Japanese

Avizo User's Guide translated to Japanese

Demo, Misc

11 May 2020 - You will find here a selection of Avizo tutorials translated to Japanese.

Molar Segmentation Using Watershed and Top-Hat and Surface Generation

Molar Segmentation Using Watershed and Top-Hat and Surface Generation

Project (hx, pgo), Demo, Data

11 May 2020 - Data, tutorial, and complete project for segmenting a CT-scanned human molar artifact. The tutorial and project cover advanced image segmentation and surface generation.

Amira User's Guide translated to Japanese

Amira User's Guide translated to Japanese

Demo, Misc

29 Jan 2020 - You will find here a large selection of Amira tutorials translated to Japanese.

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.

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.

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.

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.

Size distribution of Nb-Cu nanoparticles

Size distribution of Nb-Cu nanoparticles

Recipe ISP (hxisp,a2d), Demo, Data

26 Jun 2019 - The recipe segments the Nb particles and the Cu particles.

Porous silicon

Porous silicon

Recipe ISP (hxisp,a2d), Demo, Data

26 Jun 2019 - The recipe detects pores in a porous silicon.

Porosity in a battery separator

Porosity in a battery separator

Recipe ISP (hxisp,a2d), Demo, Data

26 Jun 2019 - The recipe classifies the pores in a battery separator (SEM image).

Porosity in a polymer divider

Porosity in a polymer divider

Recipe ISP (hxisp,a2d), Demo, Data

26 Jun 2019 - The recipe detects pores in a polymer divider (SEM image).

Particle agglomeration

Particle agglomeration

Recipe ISP (hxisp,a2d), Demo, Data

26 Jun 2019 - The recipe segments particles that are touching each other, and individual ones.