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.

FIBSEM Mitochondria Segmentation
Add-on How-to

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
Add-on How-to

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.

AMIRA_LOCAL Setup Tutorial
How-to

AMIRA_LOCAL Setup Tutorial

Demo

5 Oct 2020 - Brief video explaining how to set up an AMIRA_LOCAL path on Windows 10.

Segmentation of pathological osteocytes present in an undecalcified piece of bone from mice using Amira2D
Add-on

Segmentation of pathological osteocytes present in an undecalcified piece of bone from mice using Amira2D

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
Add-on

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)

Porous Silicon Batch
Add-on

Porous Silicon Batch

Recipe ISP (hxisp,a2d), Data

18 Sep 2019 - Batch processing of a subset of porous silicon SEM images.

Three Phase Ti Segmentation
Add-on

Three Phase Ti Segmentation

Recipe ISP (hxisp,a2d), Data

24 Jul 2019 - Alpha, Borides, Beta segmentation of FIB Serial Section Dataset of Ti Alloy with Borides

Plates in Ti-62222
Add-on

Plates in Ti-62222

Recipe ISP (hxisp,a2d), Data

24 Jul 2019 - FIB Serial Section of Ti-62222

Particles identification in Nickel-Base Superalloy
Add-on

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 for Image Segmentation
Add-on

Getting Started with Deep Learning Training for Image 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
Add-on

Size distribution of Nb-Cu nanoparticles

Recipe ISP (hxisp,a2d), Data

26 Jun 2019 - The recipe segments the Nb particles and the Cu particles.

Porous Silicon
Add-on

Porous Silicon

Recipe ISP (hxisp,a2d), Data

26 Jun 2019 - The recipe detects pores in a porous silicon.

Porosity in a Battery Separator
Add-on

Porosity in a Battery Separator

Recipe ISP (hxisp,a2d), Data

26 Jun 2019 - The recipe classifies the pores in a battery separator (SEM image).

Porosity in a Polymer Divider
Add-on

Porosity in a Polymer Divider

Recipe ISP (hxisp,a2d), Demo, Data

26 Jun 2019 - The recipe detects pores in a polymer divider (SEM image).

Particle Agglomeration
Add-on

Particle Agglomeration

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
Add-on

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).

Au-Ni-Cl Nanoparticles
Add-on

Au-Ni-Cl Nanoparticles

Recipe ISP (hxisp,a2d)

25 Jun 2019 - This recipe segments nanoparticles of different element from an EDS map.

BSE SEM denoiser
Add-on

BSE SEM denoiser

Deep learning model

21 Jun 2019 - U-Net model for denoising back-scattered SEM images.

Polymer Beads
Add-on

Polymer Beads

Recipe ISP (hxisp,a2d)

6 Jun 2019 - Segmentation of the particles located in the foreground of the SEM image.