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.

How to Customize Amira-Avizo with moduleExtender NEW
Add-on How-to

How to Customize Amira-Avizo with moduleExtender

Tcl, Misc

25 Nov 2021 - Are there module settings you always need to change during your daily work? This Xtra describes how you can permanently change default settings of modules in Amira-Avizo.

Masking Map by Molecule NEW
Add-on

Masking Map by Molecule

Tcl

18 Nov 2021 - Module Mask Map By Molecule lets you mask an EM map of a macro molecule by an atomic model of the entire or partial molecule. This can be useful when validating EM maps from SPA with published models from the Protein Data Bank.

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.

Differential Interference Contrast (DIC) Image Segmentation and Quantification using Deep Learning NEW
Add-on How-to

Differential Interference Contrast (DIC) Image Segmentation and Quantification using Deep Learning

Recipe (hxrecipe), Deep learning model, Demo

18 Nov 2021 - This workflow uses deep learning to segment images obtained by Differential Interference Contrast (DIC) microscopy. Nuclei and mitochondria are segmented and counted cell per cell.

Porosity Volume Fraction Analysis NEW
Add-on How-to

Porosity Volume Fraction Analysis

Project (hx, pgo), Demo, Data

18 Nov 2021 - This tutorial demonstrates the steps to quantify porosity volume fraction and distribution.

Bookmarks Manager NEW
Add-on

Bookmarks Manager

Python (pyscro)

18 Nov 2021 - Add bookmarks to your project, including status and camera, so you can easily retrieve a given visualization. You can then navigate through the bookmarks.

Landmark based Data Alignment NEW
Add-on How-to

Landmark based Data Alignment

Tcl, Demo

18 Nov 2021 - This module can be used to facilitate the alignment of datasets using pairs of landmarks. The video tutorial demonstrates this technique.

Inter Time Steps Recipe Player NEW
Add-on How-to

Inter Time Steps Recipe Player

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

18 Nov 2021 - The Inter Time Steps Recipe Player module executes a two-input recipe to a specific pair of two successive time steps of a time series dataset, or to all its pairs of two successive time steps.

How to Script the Instantiation of a Python Script Object Xtra
Add-on How-to

How to Script the Instantiation of a Python Script Object Xtra

Python (pyscro)

9 Sep 2021 - This Xtra provides a script template that can be used to instantiate a Python script object Xtra from the Python console or from a Python script.

Using Tcl Command Module for Multi-File OBJ Export
Add-on How-to

Using Tcl Command Module for Multi-File OBJ Export

Tcl, Project (hx, pgo)

7 Sep 2021 - The Tcl Command Module makes it easy to export the surfaces of single objects from a multi-object surface as OBJ (Wavefront) files.

Split and Merge Segments
Add-on How-to

Split and Merge Segments

XPand module

29 Jun 2021 - The Split and Merge Segments module merges the two most representative segments at the intersection points of a graph structure and detaches the others.

Browse TensorBoard of old Deep Learning Training sessions
Add-on

Browse TensorBoard of old Deep Learning Training sessions

Deep learning model, Python (pyscro)

21 May 2021 - This Xtra contains a module that allows you to browse TensorBoard logs from previous Deep Learning Training sessions.

Add Data To Point Cloud
Add-on

Add Data To Point Cloud

Python (pyscro)

29 Mar 2021 - AddDataToPointCloud writes data defined on mesh-nodes into a point-cloud with an equal number of points. Together with the "PointCloudToSpreadsheet" Xtra, this module can be used, for example, to export the results created by the Surface Distance module.

Extract Oriented Labels
Add-on How-to

Extract Oriented Labels

Python (pyscro), Project (hx, pgo)

29 Mar 2021 - The Extract Oriented Labels module extracts every label from the input label image, and resamples each image along its own main orientations (or eigenvectors).

Fitting Molecule To Map
Add-on

Fitting Molecule To Map

Tcl

8 Mar 2021 - This Xtra contains a script module to fit molecular models to density maps, a process frequently called "docking".

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.

Getting Started with Flatten Module
Add-on How-to

Getting Started with Flatten Module

Project (hx, pgo), Demo

8 Mar 2021 - This tutorial demonstrates use of the Flatten experimental module to create interactive contours by defining the unfolding surface while respecting the constraints of the module inputs.

Large Data Visualization
Add-on How-to

Large Data Visualization

Demo, Misc

24 Feb 2021 - This video tutorial demonstrates how to deal with visualization of large datasets.

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.

High Content Screening Plate Manager
Add-on

High Content Screening Plate Manager

Python (pyscro), Tcl

12 Feb 2021 - Load, visualize and process multi-channel fields from Thermo Scientific CellInsight CX5, CX7 LED and CX7 LZR HCA instruments and HCS Studio software.