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.

Non-Standard Python Package Installation Tutorial
How-to

Non-Standard Python Package Installation Tutorial

Demo, Misc

13 Jan 2021 - Brief video explaining how to install a Python package in a newly created Python environment using pip or edm.

FIBSEM Mitochondria Segmentation
Add-on How-to

FIBSEM Mitochondria Segmentation

Deep learning model

12 Jan 2021 - Pre-trained model for the Deep Learning Prediction module detecting mitochondria in a Focused Ion Beam Scanning Electron Microscope (FIBSEM) data set.

Multi-Component Analysis of X-ray Computed Tomography Datasets
Add-on How-to

Multi-Component Analysis of X-ray Computed Tomography Datasets

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

4 Jan 2021 - The following videos and training material detail the steps taken to automate the analysis of multiple parts in a single X-ray CT volume.

Analysis of X-ray CT Calibration Spheres using the Metrology Workroom
How-to

Analysis of X-ray CT Calibration Spheres using the Metrology Workroom

Demo, Data, Misc

4 Jan 2021 - This video presents how to use the Metrology workroom to analyze calibration spheres used in X-ray Computed Tomography.

Thresholding From Mean
Add-on How-to

Thresholding From Mean

Python (pyscro), Data

4 Jan 2021 - This module performs an adaptive global thresholding of the input image by computing a deviation from the mean of its grayscale values.

How to Create and Animate a Camera Path
How-to

How to Create and Animate a Camera Path

Demo

3 Jan 2021 - This tutorial explains how to create a camera path, and then animate the camera along this path with the Animation Director.

How to Animate the Appearance of Objects with the Animation Director
How-to

How to Animate the Appearance of Objects with the Animation Director

Demo

3 Jan 2021 - This tutorial explains how to animate the appearance and disappearance of objects with the Animation Director.

How to Get Started with the Animation Director
How-to

How to Get Started with the Animation Director

Demo

3 Jan 2021 - This tutorial demonstrates the basic techniques of animation creation with the Animation Director.

Export Measures
Add-on

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.

Marker Based Watershed Recipe
Add-on

Marker Based Watershed Recipe

Recipe ISP (hxisp,a2d)

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

Automatic extraction of surface cross section
Add-on

Automatic extraction of surface cross section

Python (pyscro), Project (hx, pgo)

20 Oct 2020 - Create partially transparent capping surfaces

Auto Threshold for Multi-Thresholding
Add-on

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".

Volume Projection
Add-on

Volume Projection

Python (pyscro)

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

Relative Area Fraction for Amira-Avizo2D
Add-on How-to

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.

AMIRA_LOCAL Setup Tutorial
How-to

AMIRA_LOCAL Setup Tutorial

Demo

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

Explode Surface Animation Script
Add-on

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.

PerGeos Process Based Modelling
Add-on

PerGeos Process Based Modelling

XPand module

4 Sep 2020 - Process Based Modelling modules for PerGeos

Apply a Recipe on a Batch of Files
Add-on

Apply a Recipe on a Batch of Files

Recipe (hxrecipe), Tcl

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

Selective Border Kill
Add-on

Selective Border Kill

Tcl

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

2D Cell Tracking Example
Add-on

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.

Segmentation of agglomerated Ni nanoparticles
Add-on

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