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.

BSE SEM denoiser

BSE SEM denoiser

Deep learning model

U-Net model for denoising back-scattered SEM images.

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How to use PyQt5 in a pyscro module

How to use PyQt5 in a pyscro module

Python (pyscro)

This example shows how to use PyQt5 in a pyscro module.

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Parameter optimization for auto-thresholding a data

Parameter optimization for auto-thresholding a data

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

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

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Amira User's Guide translated to Japanese

Amira User's Guide translated to Japanese

Demo, Misc

You will find here a selection of Amira tutorials translated to Japanese.

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Feature segmentation for non-uniform illumination and low-contrast images

Feature segmentation for non-uniform illumination and low-contrast images

Recipe (hxrecipe)

The recipe lets you segment small features on images with non-uniform illumination and low contrast.

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Porosity Clustering Analysis and Distance to Surface

Porosity Clustering Analysis and Distance to Surface

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

This tutorial demonstrates the steps to quantify porosity distribution and the distance to surface analysis.

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Refine Surface

Refine Surface

XPand module

Module for refining a surface.

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Recipe Sequencer

Recipe Sequencer

Recipe (hxrecipe), XPand module, Data

Module for sequencing a recipe on each individual isolated label from a label field.

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

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

Python (pyscro)

This script simply reads and loads numpy arrays in a user specified directory into PerGeos/Amira-Avizo as an image.

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Length Distribution Analysis

Length Distribution Analysis

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

This tutorial demonstrated how to quantify thickness distribution along the length

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Export Spatial Graph to MS Excel XML document

Export Spatial Graph to MS Excel XML document

Recipe (hxrecipe), Tcl, Demo

An Amira-Avizo recipe to export to a XML document which can be used in MS Excel for further analysis.

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Create Label Annotations

Create Label Annotations

Tcl

This module creates label annotations from the result of a Label Analysis with the help of the Measurement tool.

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Average interleaved data

Average interleaved data

Python (pyscro), Project (hx, pgo)

The purpose of this python script object is to average interleaved data.

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Auto-Crop script module

Auto-Crop script module

Tcl

Automatically crop your volume data to reduce its size.

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View Manager

View Manager

Tcl

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

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How to use deep learning models in AmiraAvizo2D Analyzer

How to use deep learning models in AmiraAvizo2D Analyzer

Recipe ISP (hxisp,a2d), Deep learning model, Data

Examples showing how to use AI (deep learning models) in an Analyzer recipe (hxisp)

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Getting Started with Deep Learning Training (Membrane Segmentation)

Getting Started with Deep Learning Training (Membrane Segmentation)

Deep learning model, Project (hx, pgo), Data

Model and companion project for the Deep Learning tutorial.

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