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.
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Extract Oriented Labels NEW
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 NEW
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) NEW
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 NEW
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 NEW
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 NEW
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 NEW
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 NEW
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 NEW
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 NEW
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 NEW
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 NEW
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 NEW
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.

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

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 short 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 short 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 short tutorial will take you through the basis of animation creation with the Animation Director.