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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NEW Component verification using X-ray Computed Tomography and CAD comparison

Component verification using X-ray Computed Tomography and CAD comparison

Demo

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.

NEW Large Data Visualization

Large Data Visualization

Demo, Misc

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

NEW Patch Extraction Tools for Deep Learning data preparation

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.

NEW Efficient Graph-based 2D Image Segmentation

Efficient Graph-based 2D Image Segmentation

XPand module

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

NEW Point Cloud to Spreadsheet

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.

NEW Non-Standard Python Package Installation Tutorial

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.

NEW Multi-component analysis of X-ray Computed Tomography datasets

Multi-component analysis of X-ray Computed Tomography datasets

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

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.

NEW Analysis of X-ray CT calibration spheres using the Metrology workroom

Analysis of X-ray CT calibration spheres using the Metrology workroom

Demo

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

NEW Thresholding From Mean

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.

Export Measures

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

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

Automatic extraction of surface cross section

Python (pyscro), Project (hx, pgo)

20 Oct 2020 - Create partially transparent capping surfaces

Auto Threshold for Multi-Thresholding

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

Volume Projection

Python (pyscro)

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

Relative Area Fraction for Amira-Avizo2D

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

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

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.

Apply a Recipe on a Batch of Files

Apply a Recipe on a Batch of Files

Recipe (hxrecipe), Tcl

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

Selective Border Kill

Selective Border Kill

Tcl

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

Segmentation of agglomerated Ni nanoparticles

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

Hough Circle Fitting

Hough Circle Fitting

Python (pyscro)

30 Jul 2020 - Generalized Hough transform to fit circles to the image.