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.
Non-Standard Python Package Installation Tutorial
Demo, Misc
13 Jan 2021 - Brief video explaining how to install a Python package in a newly created Python environment using pip or edm.
FIBSEM Mitochondria Segmentation
Deep learning model
12 Jan 2021 - Pre-trained model for the Deep Learning Prediction module detecting mitochondria in a Focused Ion Beam Scanning Electron Microscope (FIBSEM) data set
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.
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".
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.
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.