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.

How to Use the Image Stack Processing (ISP) Workroom NEW
How-to

How to Use the Image Stack Processing (ISP) Workroom

Demo

14 Sep 2021 - This tutorial demonstrates how to use the ISP workroom, an intuitive 2D workroom for automating image processing workflows in 3D.

How to Overlay Images Using the Color Wash module NEW
How-to

How to Overlay Images Using the Color Wash module

Demo

14 Sep 2021 - This short video demonstrates how to use the Color Wash module to overlay label colors onto a greyscale image.

How to Register and Merge Images NEW
How-to

How to Register and Merge Images

Demo

14 Sep 2021 - This short tutorial demonstrates how to use the Register Images and Merge modules to align and merge two images.

How to use the Transform Editor NEW
How-to

How to use the Transform Editor

Demo

14 Sep 2021 - This tutorial introduces the concept of geometric transformation in Amira-Avizo and demonstrates data alignment with the Transform Editor.

How to Create a Custom Label Colormap NEW
How-to

How to Create a Custom Label Colormap

Demo

14 Sep 2021 - This short video explains how to create and export a label colormap from the Segmentation Editor.

How to Change the Label Colormap to display a Label Field NEW
How-to

How to Change the Label Colormap to display a Label Field

Demo

14 Sep 2021 - This short video explains how to set an appropriate colormap for label fields with a large number of labels.

How to Edit a Colormap from the Colormap Editor NEW
How-to

How to Edit a Colormap from the Colormap Editor

Demo

14 Sep 2021 - This tutorial demonstrates how to use the Colormap Editor.

How to Save a Project NEW
How-to

How to Save a Project

Demo

14 Sep 2021 - This short video presents the different options to save a project.

Extract Oriented Labels
Add-on How-to

Extract Oriented Labels

Python (pyscro), Project (hx, pgo)

29 Mar 2021 - This module extracts each single label from the input label image and resamples each of it along its own main orientations (or eigenvectors).

Fitting Molecule To Map
Add-on

Fitting Molecule To Map

Tcl

8 Mar 2021 - Script module to fit molecular models to density maps, a process frequently called "docking".

Image Segmentation Evaluation Using Standard Metrics (Python)
Add-on

Image Segmentation Evaluation Using Standard Metrics (Python)

Python (pyscro), Project (hx, pgo)

8 Mar 2021 - Segmentation evaluation using standard precision, recall metrics for comparing two segmentation labels.

Component Verification Using X-ray Computed Tomography and CAD Comparison
How-to

Component Verification Using X-ray Computed Tomography and CAD Comparison

Demo, Data, Misc

3 Mar 2021 - The following video and training material will use an additively manufactured con rod to demonstrate how the surface profile generated from X-ray CT data can be compared to the original component CAD design.

Large Data Visualization
Add-on How-to

Large Data Visualization

Demo, Misc

24 Feb 2021 - This video tutorial demonstrates how to deal with visualization of large datasets.

Patch Extraction Tools for Deep Learning data preparation
Add-on

Patch Extraction Tools for Deep Learning data preparation

Python (pyscro)

22 Feb 2021 - A set of tools dedicated to preparation of data for training Deep Learning models and reducing annotation time.

How to Set Up Two-Sided Clipping
How-to

How to Set Up Two-Sided Clipping

Demo

15 Feb 2021 - This short tutorial explains how to set up two-sided clipping in order to transition between two visualization of data.

How to Use Camera Orbit and Animate a Rotation
How-to

How to Use Camera Orbit and Animate a Rotation

Demo

15 Feb 2021 - This short tutorial explains how to use the Camera Orbit module and then animate the rotation around an object in the Animation Director.

High Content Screening Plate Manager
Add-on

High Content Screening Plate Manager

Python (pyscro), Tcl

12 Feb 2021 - Load, visualize and process multi-channel fields from Thermo Scientific CellInsight CX5, CX7 LED and CX7 LZR HCA instruments and HCS Studio software.

How to Create a Movie File
How-to

How to Create a Movie File

Demo

10 Feb 2021 - This tutorial explains how to export a movie file from the Animation Director.

How to Compare Slices Side by Side
How-to

How to Compare Slices Side by Side

Demo

10 Feb 2021 - This short tutorial explains how to compare side by side two slices displaying different information, for example of raw data and its corresponding labeled image.

Point Cloud to Spreadsheet
Add-on

Point Cloud to Spreadsheet

Python (pyscro)

22 Jan 2021 - With this Python script-object you can convert a point-cloud object to a spreadsheet object.

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.