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 Script the Instantiation of a Python Script Object Xtra NEW
Add-on How-to

How to Script the Instantiation of a Python Script Object Xtra

Python (pyscro)

9 Sep 2021 - This Xtra provides a script template that can be used to instantiate a Python script object Xtra from the Python console or from a Python script.

Using Tcl Command Module for Multi-File OBJ Export
Add-on How-to

Using Tcl Command Module for Multi-File OBJ Export

Tcl, Project (hx, pgo)

7 Sep 2021 - The Tcl Command Module makes it easy to export the surfaces of single objects from a multi-object surface as OBJ (Wavefront) files.

Xplore5D Tutorial Data
How-to

Xplore5D Tutorial Data

Data

8 Jul 2021 - This Xtra provides the data used in the tutorials for the Xplore5D extension, available in Amira-Avizo 2021.1

Split and Merge Segments
Add-on How-to

Split and Merge Segments

XPand module

29 Jun 2021 - The Split and Merge Segments module merges the two most representative segments at the intersection points of a graph structure and detaches the others.

More Resources on Amira-Avizo Learning Center YouTube Playlist
How-to

More Resources on Amira-Avizo Learning Center YouTube Playlist

Demo, Misc

4 Jun 2021 - This Xtra provides links to Amira-Avizo Learning Center YouTube playlist.

Browse TensorBoard of old Deep Learning Training sessions
Add-on

Browse TensorBoard of old Deep Learning Training sessions

Deep learning model, Python (pyscro)

21 May 2021 - This Xtra contains a module that allows you to browse TensorBoard logs from previous Deep Learning Training sessions.

Add Data To Point Cloud
Add-on

Add Data To Point Cloud

Python (pyscro)

29 Mar 2021 - AddDataToPointCloud writes data defined on mesh-nodes into a point-cloud with an equal number of points. Together with the "PointCloudToSpreadsheet" Xtra, this module can be used, for example, to export the results created by the Surface Distance module.

Extract Oriented Labels
Add-on How-to

Extract Oriented Labels

Python (pyscro), Project (hx, pgo)

29 Mar 2021 - The Extract Oriented Labels module extracts every label from the input label image, and resamples each image along its own main orientations (or eigenvectors).

Fitting Molecule To Map
Add-on

Fitting Molecule To Map

Tcl

8 Mar 2021 - This Xtra contains a 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, and recall metrics for comparing two segmentation labels.

Getting Started with Flatten Module
Add-on How-to

Getting Started with Flatten Module

Project (hx, pgo), Demo

8 Mar 2021 - This tutorial demonstrates use of the Flatten experimental module to create interactive contours by defining the unfolding surface while respecting the constraints of the module inputs.

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 uses 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 the 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 tutorial explains how to set up two-sided clipping in order to transition between two visualizations 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 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.

Efficient Graph-based 2D Image Segmentation
Add-on

Efficient Graph-based 2D Image Segmentation

XPand module

12 Feb 2021 - This Xtra implements efficient graph-based image segmentation by Felzenszwalb and Huttenlocher.

How to Create a Movie File
How-to

How to Create a Movie File

Demo

10 Feb 2021 - This tutorial explains how to create and 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 tutorial explains how to perform a side-by-side comparison of two slices that display 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 - This Python script-object allows you to convert a point-cloud object to a spreadsheet object.