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
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.
Recipe ISP (hxisp,a2d)
3 Jul 2020 - This is a workflow to segment out osteocytes present in mouse bone sample using Amira2D
How to use deep learning models in AmiraAvizo2D Analyzer
Recipe ISP (hxisp,a2d), Deep learning model, Data
3 Oct 2019 - Examples showing how to use AI (deep learning models) in an Analyzer recipe (hxisp)
Recipe ISP (hxisp,a2d), Data
18 Sep 2019 - Batch processing of a subset of porous silicon SEM images.
Recipe ISP (hxisp,a2d), Data
24 Jul 2019 - Alpha, Borides, Beta segmentation of FIB Serial Section Dataset of Ti Alloy with Borides
Recipe ISP (hxisp,a2d), Data
24 Jul 2019 - FIB Serial Section of Ti-62222
Particles identification in Nickel-Base Superalloy
Recipe ISP (hxisp,a2d), Python (pyscro), Data
24 Jul 2019 - FIB Serial Section of Particles in Nickel-Base Superalloy
Getting Started with Deep Learning Training (Membrane Segmentation)
Deep learning model, Project (hx, pgo), Data
27 Jun 2019 - Model and companion project for the Deep Learning tutorial.
Size distribution of Nb-Cu nanoparticles
Recipe ISP (hxisp,a2d), Data
26 Jun 2019 - The recipe segments the Nb particles and the Cu particles.
Recipe ISP (hxisp,a2d), Data
26 Jun 2019 - The recipe detects pores in a porous silicon.
Porosity in a Battery Separator
Recipe ISP (hxisp,a2d), Data
26 Jun 2019 - The recipe classifies the pores in a battery separator (SEM image).
Recipe ISP (hxisp,a2d), Demo, Data
26 Jun 2019 - The recipe detects pores in a polymer divider (SEM image).
Recipe ISP (hxisp,a2d), Data
26 Jun 2019 - The recipe segments particles that are touching each other, and individual ones.
Automated sizing of large area nanoparticles
Recipe ISP (hxisp,a2d), Python (pyscro)
25 Jun 2019 - The recipe segments large area Pt-Rh nanoparticles at high resolution (TEM image).
Recipe ISP (hxisp,a2d)
25 Jun 2019 - This recipe segments nanoparticles of different element from an EDS map.
Deep learning model
21 Jun 2019 - U-Net model for denoising back-scattered SEM images.
Recipe ISP (hxisp,a2d)
6 Jun 2019 - Segmentation of the particles located in the foreground of the SEM image.