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.
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.
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.
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
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
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 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.
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.
Recipe (hxrecipe), Project (hx, pgo), Demo, Data
21 Oct 2019 - This tutorial demonstrated how to quantify thickness distribution along the length