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.
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.
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.
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".
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
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
Segment TEM data without artifact and background effect
Recipe (hxrecipe), Tcl, Project (hx, pgo)
10 Jul 2020 - Segment TEM data aided by the Structure enhancement filter.
Porosity and Permeability by blocks
Tcl
3 Jul 2020 - Splits a binary pore space into blocks and output one porosity and permeability value for every block
Tcl, Project (hx, pgo), Data
17 Jun 2020 - To make use of XFiber, the user usually needs to input many parameters. This package provides 2 tools to ease Xfiber process by presetting Cylinder Correlation and Auto Trace Correlation modules values.
Copy Measure Annotation Settings
Tcl
15 Apr 2020 - This Tcl script-object can be used to copy visualisation settings from one measure to all others in a Measurement module. It is also possible to save/load settings to/from a text file.
Tcl
15 Apr 2020 - Use this module to fill the text field of a Caption module with the value of a port of another module.
Tcl
13 Dec 2019 - This module creates label annotations from the result of a Label Analysis with the help of the Measurement tool.
Tcl
16 Oct 2019 - Automatically crop your volume data to reduce its size.
Simulation-based Tortuosity estimation of porous media
Tcl
16 Oct 2019 - Tortuosity is a key factor for material characterization of porous media. This package propose 4 methods to calculate the tortuosity factor based on the xlab properties: Absolute Permeability, Molecular Diffusion, Formation Factor and Thermal Conductivity.
PerGeos TCL script for processing all files in a folder with a recipe
Tcl
16 Oct 2019 - Process all files in a folder by applying the same recipe to all of them individually.
Export Spatial Graph to MS Excel XML document
Recipe (hxrecipe), Tcl, Demo
16 Oct 2019 - An Amira-Avizo recipe to export to a XML document which can be used in MS Excel for further analysis.
Tcl
14 Oct 2019 - This module allows storing and retrieving camera settings for viewer windows to be able to switch easily between different view presets.