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.

Facies Classification from Well Logs NEW
Add-on How-to

Facies Classification from Well Logs

Python (pyscro), Demo

3 Dec 2021 - Facies (rock type) classification from well logs using supervised machine learning algorithms.

kMeans Clustering on Label Analysis (Python) NEW
Add-on

kMeans Clustering on Label Analysis (Python)

Python (pyscro)

18 Nov 2021 - This Xtra implements kMeans clustering on a label analysis spreadsheet. Separated objects can be clustered based on any measure group that is inbuilt or user customized.

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

Image Segmentation Evaluation Using Standard Metrics (Python)

Python (pyscro), Project (hx, pgo)

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

Patch Extraction Tools for Deep Learning data preparation
Add-on

Patch Extraction Tools for Deep Learning data preparation

Python (pyscro)

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

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 by means of Python scripts.

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.