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.

Image Segmentation Evaluation Using Standard Metrics (Python) NEW
Add-on

Image Segmentation Evaluation Using Standard Metrics (Python)

Python (pyscro), Project (hx, pgo)

8 Mar 2021 - Segmentation evaluation using standard precision, recall metrics for comparing two segmentation labels.

Large Data Visualization NEW
Add-on How-to

Large Data Visualization

Demo, Misc

24 Feb 2021 - This video tutorial demonstrates how to deal with visualization of large datasets.

Patch Extraction Tools for Deep Learning data preparation NEW
Add-on

Patch Extraction Tools for Deep Learning data preparation

Python (pyscro)

22 Feb 2021 - A set of tools dedicated to preparation of data for training Deep Learning models and reducing annotation time.

Non-Standard Python Package Installation Tutorial
How-to

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.

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.

PerGeos Process Based Modelling
Add-on

PerGeos Process Based Modelling

XPand module

4 Sep 2020 - Process Based Modelling modules for PerGeos

CylinderSlice with Native resolution in Z
Add-on

CylinderSlice with Native resolution in Z

XPand module

10 Jul 2020 - This module allows the native resolution in the Z axis for the Cylinder Slice.

Optical Thin Section Pore Space Characterization in HSV colorspace
Add-on

Optical Thin Section Pore Space Characterization in HSV colorspace

Python (pyscro), Project (hx, pgo), Data

10 Jul 2020 - Optical Thin Section Pore Space is segmented converting RGBA images in HSV colorspace via Python scripts.

Porosity and Permeability by blocks
Add-on

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

Extract Label
Add-on

Extract Label

Python (pyscro)

11 May 2020 - This module extracts a specified label region by the ID Supports 8, 16 and 32 bit label

Scale-Space Laplacian of Gaussian Filter
Add-on

Scale-Space Laplacian of Gaussian Filter

Python (pyscro)

15 Apr 2020 - Image processing filter enhancing spherical or blob like objects of various sizes.

Load a Numpy array into PerGeos/Amira-Avizo using the Python API
Add-on

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
Add-on

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.

Eagleford Shale FIB-SEM Segmentation
Add-on

Eagleford Shale FIB-SEM Segmentation

Recipe (hxrecipe)

17 Oct 2019 - This recipe guided workflow will result in a 5-phase segmentation applicable to the included dataset and most typical FIB-SEM data. Input Data, the Recipe, Output data are included here.

PerGeos TCL script for processing all files in a folder with a recipe
Add-on

PerGeos TCL script for processing all files in a folder with a recipe

Tcl

16 Oct 2019 - Process all files in a folder by applying the same recipe to all of them individually.

View Manager
Add-on

View Manager

Tcl

14 Oct 2019 - This module allows storing and retrieving camera settings for viewer windows to be able to switch easily between different view presets.

Berea Pore Size Distribution Tutorial
Add-on How-to

Berea Pore Size Distribution Tutorial

Recipe (hxrecipe), Project (hx, pgo), Demo, Data

11 Oct 2019 - Create a semi-automatic workflow for Pore Size Distribution on Berea sandstone

Getting Started with Deep Learning Training
Add-on

Getting Started with Deep Learning Training

Deep learning model, Data

5 Sep 2019 - Model and companion project for the Deep Learning tutorial.

BSE SEM denoiser
Add-on

BSE SEM denoiser

Deep learning model

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