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.
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.
Recipe ISP (hxisp,a2d)
3 Jul 2020 - This is a workflow to segment out osteocytes present in mouse bone sample using Amira2D
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
Extracting and Visualizing Local Statistics from Fibrous Materials
Project (hx, pgo)
3 Jul 2020 - This XTRA entry discusses the application of the “Spatial Graph Local Statistics” to extract statistical information from traced fibers in a fibrous material. The sample is 50% glass fiber-reinforced polymer (GFRP), courtesy of EMS Grivory.
Interactive Top-Hat by Reconstruction.
XPand module
3 Jul 2020 - This module provides an interactive Top-Hat segmentation that prevents from segmenting false positive porosity on the edges.
Imaging Codec for thumbnails in Windows Explorer
Misc
24 Jun 2020 - Codec enabling thumbnails for .am images in Windows Explorer
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.
Avizo User's Guide translated to Japanese
Demo, Misc
11 May 2020 - You will find here a selection of Avizo tutorials translated to Japanese.
Molar Segmentation Using Watershed and Top-Hat and Surface Generation
Project (hx, pgo), Demo, Data
11 May 2020 - Data, tutorial, and complete project for segmenting a CT-scanned human molar artifact. The tutorial and project cover advanced image segmentation and surface generation.
Python (pyscro)
11 May 2020 - This module extracts a specified label region by the ID Supports 8, 16 and 32 bit label
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.
Scale-Space Laplacian of Gaussian Filter
Python (pyscro)
15 Apr 2020 - Image processing filter enhancing spherical or blob like objects of various sizes.
Amira User's Guide translated to Japanese
Demo, Misc
29 Jan 2020 - You will find here a large selection of Amira tutorials translated to Japanese.
Tcl
13 Dec 2019 - This module creates label annotations from the result of a Label Analysis with the help of the Measurement tool.
Python (pyscro), Project (hx, pgo)
21 Oct 2019 - The purpose of this python script object is to average interleaved data.
2D SEM (White) Grain Segmentation
Recipe (hxrecipe), Data
21 Oct 2019 - This recipe segments and calculate the physical attributes of the white grains in the 2D SEM image
Load a Numpy array into PerGeos/Amira-Avizo using the Python API
Python (pyscro)
21 Oct 2019 - This script simply reads and loads numpy arrays in a user specified directory into PerGeos/Amira-Avizo as an image.
Random Forests for Multiclass Segmentation using Python API in PerGeos
Python (pyscro), Project (hx, pgo), Data
21 Oct 2019 - Simple demonstration of feature computation where the feature vector contains intensity and 2D eigenvalues (X & Y). This example uses random forests implementation from the sklearn package.
Recipe (hxrecipe), Project (hx, pgo), Demo, Data
21 Oct 2019 - This tutorial demonstrated how to quantify thickness distribution along the length
Porosity Clustering Analysis and Distance to Surface
Recipe (hxrecipe), Project (hx, pgo), Demo, Data
21 Oct 2019 - This tutorial demonstrates the steps to quantify porosity distribution and the distance to surface analysis.