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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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.
Multi-Scale Cylinder Correlation
Python (pyscro), Project (hx, pgo)
30 Jul 2020 - This module gives better results for fiber-tracing in the case of multiple fibers with differing or varying diameters in the same dataset.
Create a porosity analysis recipe
Recipe (hxrecipe), Demo
15 Jul 2020 - This tutorial explains how to create a simple porosity analysis and turn it into a push-button recipe.
CylinderSlice with Native resolution in Z
XPand module
10 Jul 2020 - This module allows the native resolution in the Z axis for the Cylinder Slice.
Optical Thin Section Pore Space Characterization in HSV colorspace
Python (pyscro), Project (hx, pgo), Data
10 Jul 2020 - Optical Thin Section Pore Space is segmented converting RGBA images in HSV colorspace via Python scripts.