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.

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.

Extract Label

Extract Label

Python (pyscro)

11 May 2020 - This module extracts a specified label region by the ID Supports 8, 16 and 32 bit label

Copy Measure Annotation Settings

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

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

Scale-Space Laplacian of Gaussian Filter

Python (pyscro)

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

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).

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.

Create Label Annotations

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.

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.

Random Forests for Multiclass Segmentation using Python API in PerGeos

Random Forests for Multiclass Segmentation using Python API in PerGeos

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

21 Oct 2019 - Simple demonstration of feature computation where the feature vector contains intensity and 2D eigenvalues (X & Y). This example uses random forests implementation from the sklearn package.

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.