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.

How to use PyQt5 in a pyscro module
Add-on

How to use PyQt5 in a pyscro module

Python (pyscro)

7 Oct 2019 - This example shows how to use PyQt5 in a pyscro module.

Parameter optimization for auto-thresholding a data
Add-on

Parameter optimization for auto-thresholding a data

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

7 Oct 2019 - In this pyscro example we use opencv and matplotlib to automatically calculate an optimized parameter for thresholding the data based on various metrics.

Hough Circle Fitting
Add-on

Hough Circle Fitting

Python (pyscro)

30 Jul 2020 - Generalized Hough transform to fit circles to the image.

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.

Volume Projection
Add-on

Volume Projection

Python (pyscro)

19 Oct 2020 - Volume projection along any orthogonal axis using arithmetic operations.

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.

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.