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.
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
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.
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
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
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
Demo
3 Jan 2021 - This short tutorial will take you through the basis of animation creation with the Animation Director.
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.
Recipe ISP (hxisp,a2d)
17 Nov 2020 - Recipe for Marker Based Watershed as in the Segmentation Editor
Automatic extraction of surface cross section
Python (pyscro), Project (hx, pgo)
20 Oct 2020 - Create partially transparent capping surfaces
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".
Python (pyscro)
19 Oct 2020 - Volume projection along any orthogonal axis using arithmetic operations.
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.
Demo
5 Oct 2020 - Brief video explaining how to set up an AMIRA_LOCAL path on Windows 10.
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
XPand module
4 Sep 2020 - Process Based Modelling modules for PerGeos
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.
Tcl
24 Aug 2020 - Filter particles based on their contact with each border of the image
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
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
Cell Detection and Tracking 2020.2
Recipe ISP (hxisp,a2d), Python (pyscro), Project (hx, pgo), Demo
21 Aug 2020 - Simple workflow for tracking cell nuclei in a 3D Time Series.
Python (pyscro)
30 Jul 2020 - Generalized Hough transform to fit circles to the image.