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 Point Cloud to Spreadsheet

Point Cloud to Spreadsheet

Python (pyscro)

22 Jan 2021 - With this Python script-object you can convert a point-cloud object to a spreadsheet object.

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 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

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.

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.

 Imaging Codec for thumbnails in Windows Explorer

Imaging Codec for thumbnails in Windows Explorer

Misc

24 Jun 2020 - Codec enabling thumbnails for .am images in Windows Explorer