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.

Create Label Annotations
Add-on

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
Add-on

Average interleaved data

Python (pyscro), Project (hx, pgo)

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

Load a Numpy array into PerGeos/Amira-Avizo using the Python API
Add-on

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
Add-on How-to

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
Add-on How-to

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.

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

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.

Auto-Crop script module
Add-on

Auto-Crop script module

Tcl

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

Export Spatial Graph to MS Excel XML document
Add-on How-to

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
Add-on

Refine Surface

XPand module

16 Oct 2019 - Module for refining a surface.

View Manager
Add-on

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
Add-on

Recipe Sequencer

Recipe (hxrecipe), XPand module, Data

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

Parameter optimization for auto-thresholding a data
Add-on

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
Add-on

How to use PyQt5 in a pyscro module

Python (pyscro)

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

How to use deep learning models in AmiraAvizo2D Analyzer
Add-on

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)

Getting Started with Deep Learning Training (Membrane Segmentation)
Add-on

Getting Started with Deep Learning Training (Membrane Segmentation)

Deep learning model, Project (hx, pgo), Data

27 Jun 2019 - Model and companion project for the Deep Learning tutorial.

BSE SEM denoiser
Add-on

BSE SEM denoiser

Deep learning model

21 Jun 2019 - U-Net model for denoising back-scattered SEM images.