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.

NEW Non-Standard Python Package Installation Tutorial

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.

NEW FIBSEM Mitochondria Segmentation

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

NEW Multi-component analysis of X-ray Computed Tomography datasets

Multi-component analysis of X-ray Computed Tomography datasets

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

4 Jan 2021 - The following videos and training material detail the steps taken to automate the analysis of multiple parts in a single X-ray CT volume.

NEW Analysis of X-ray CT calibration spheres using the Metrology workroom

Analysis of X-ray CT calibration spheres using the Metrology workroom

Demo

4 Jan 2021 - This video presents how to use the Metrology workroom to analyze calibration spheres used in X-ray Computed Tomography.

NEW Thresholding From Mean

Thresholding From Mean

Python (pyscro), Data

4 Jan 2021 - This module performs an adaptive global thresholding of the input image by computing a deviation from the mean of its grayscale values.

NEW Export Measures

Export Measures

Tcl

17 Nov 2020 - It might be desired to export the measures and annotations created with the Measurement tool of Amira/Avizo for further analysis. This module creates a spreadsheet with the data of the measurements and annotations.

NEW Marker Based Watershed Recipe

Marker Based Watershed Recipe

Recipe ISP (hxisp,a2d)

17 Nov 2020 - Recipe for Marker Based Watershed as in the Segmentation Editor

Automatic extraction of surface cross section

Automatic extraction of surface cross section

Python (pyscro), Project (hx, pgo)

20 Oct 2020 - Create partially transparent capping surfaces

Auto Threshold for Multi-Thresholding

Auto Threshold for Multi-Thresholding

Tcl

19 Oct 2020 - The combination of Auto Thresholding and Multi-Thresholding makes it easy to create precise surfaces without additional smoothing, using Generate Surface's smoothing option "Existing Weights".

Volume Projection

Volume Projection

Python (pyscro)

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

AMIRA_LOCAL Setup Tutorial

AMIRA_LOCAL Setup Tutorial

Demo

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

Explode Surface Animation Script

Explode Surface Animation Script

Tcl

5 Oct 2020 - A script that will animate the expansion of pieces of a surface. Contains the script, documentation, an example surface, and a video of the finished result.

Apply a Recipe on a Batch of Files

Apply a Recipe on a Batch of Files

Recipe (hxrecipe), Tcl

25 Aug 2020 - Apply a recipe to a batch of files and save results in output directory.

Selective Border Kill

Selective Border Kill

Tcl

24 Aug 2020 - Filter particles based on their contact with each border of the image

2D Cell Tracking Example

2D Cell Tracking Example

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

24 Aug 2020 - A 2D cell tracking example from a multichannel time series data set. Contains a segmentation recipe, modules needed to track the cells through time, and a video of the finished result.

Segmentation of agglomerated Ni nanoparticles

Segmentation of agglomerated Ni nanoparticles

Recipe ISP (hxisp,a2d)

24 Aug 2020 - This recipe segments overlapping Ni nanoparticles on a high resolution STEM image after which a size distribution of the nanoparticles can also be computed

Cell Detection and Tracking 2020.2

Cell Detection and Tracking 2020.2

Recipe ISP (hxisp,a2d), Python (pyscro), Project (hx, pgo), Demo

21 Aug 2020 - Simple workflow for tracking cell nuclei in a 3D Time Series.

Hough Circle Fitting

Hough Circle Fitting

Python (pyscro)

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

Multi-Scale Cylinder Correlation

Multi-Scale Cylinder Correlation

Python (pyscro), Project (hx, pgo)

30 Jul 2020 - This module gives better results for fiber-tracing in the case of multiple fibers with differing or varying diameters in the same dataset.

Create a porosity analysis recipe

Create a porosity analysis recipe

Recipe (hxrecipe), Demo

15 Jul 2020 - This tutorial explains how to create a simple porosity analysis and turn it into a push-button recipe.

CylinderSlice with Native resolution in Z

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.