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 Export Measures

Export Measures

Tcl

17 Nov 2020 - It might be desired to export the measures and annotations created with the Measurement tool of Amira/Avizo for further analysis. This module creates a spreadsheet with the data of the measurements and annotations.

NEW Marker Based Watershed Recipe

Marker Based Watershed Recipe

Recipe ISP (hxisp,a2d)

17 Nov 2020 - Recipe for Marker Based Watershed as in the Segmentation Editor

NEW Automatic extraction of surface cross section

Automatic extraction of surface cross section

Python (pyscro), Project (hx, pgo)

20 Oct 2020 - Create partially transparent capping surfaces

NEW Auto Threshold for Multi-Thresholding

Auto Threshold for Multi-Thresholding

Tcl

19 Oct 2020 - The combination of Auto Thresholding and Multi-Thresholding makes it easy to create precise surfaces without additional smoothing, using Generate Surface's smoothing option "Existing Weights".

NEW Volume Projection

Volume Projection

Python (pyscro)

19 Oct 2020 - Volume projection along any orthogonal axis using arithmetic operations.

NEW Relative Area Fraction for Amira-Avizo2D

Relative Area Fraction for Amira-Avizo2D

Recipe ISP (hxisp,a2d), Python (pyscro), Data, Misc

5 Oct 2020 - This Xtra provides a module to help compute the area fraction of a label over the area of another label in Amira-Avizo2D.

NEW AMIRA_LOCAL Setup Tutorial

AMIRA_LOCAL Setup Tutorial

Demo

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

NEW Explode Surface Animation Script

Explode Surface Animation Script

Tcl

5 Oct 2020 - A script that will animate the expansion of pieces of a surface. Contains the script, documentation, an example surface, and a video of the finished result.

Apply a Recipe on a Batch of Files

Apply a Recipe on a Batch of Files

Recipe (hxrecipe), Tcl

25 Aug 2020 - Apply a recipe to a batch of files and save results in output directory.

Selective Border Kill

Selective Border Kill

Tcl

24 Aug 2020 - Filter particles based on their contact with each border of the image

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

Hough Circle Fitting

Hough Circle Fitting

Python (pyscro)

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

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.

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.

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.

Extracting and Visualizing Local Statistics from Fibrous Materials

Extracting and Visualizing Local Statistics from Fibrous Materials

Project (hx, pgo)

3 Jul 2020 - This XTRA entry discusses the application of the “Spatial Graph Local Statistics” to extract statistical information from traced fibers in a fibrous material. The sample is 50% glass fiber-reinforced polymer (GFRP), courtesy of EMS Grivory.

Interactive Top-Hat by Reconstruction.

Interactive Top-Hat by Reconstruction.

XPand module

3 Jul 2020 - This module provides an interactive Top-Hat segmentation that prevents from segmenting false positive porosity on the edges.

 Imaging Codec for thumbnails in Windows Explorer

Imaging Codec for thumbnails in Windows Explorer

Misc

24 Jun 2020 - Codec enabling thumbnails for .am images in Windows Explorer

XFiber Automation

XFiber Automation

Tcl, Project (hx, pgo), Data

17 Jun 2020 - To make use of XFiber, the user usually needs to input many parameters. This package provides 2 tools to ease Xfiber process by presetting Cylinder Correlation and Auto Trace Correlation modules values.

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.