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 Hough Circle Fitting

Hough Circle Fitting

Python (pyscro)

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

NEW 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.

NEW Create a porosity analysis recipe

Create a porosity analysis recipe

Recipe (hxrecipe), Demo, Video

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

NEW 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.

NEW Optical Thin Section Pore Space Characterization in HSV colorspace

Optical Thin Section Pore Space Characterization in HSV colorspace

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

10 Jul 2020 - Optical Thin Section Pore Space is segmented converting RGBA images in HSV colorspace via Python scripts.

NEW Segment TEM data without artifact  and background effect

Segment TEM data without artifact and background effect

Recipe (hxrecipe), Tcl, Project (hx, pgo)

10 Jul 2020 - Segment TEM data aided by the Structure enhancement filter.

NEW Segmentation of pathological osteocytes present in an undecalcified piece of bone from mice using Amira2D

Segmentation of pathological osteocytes present in an undecalcified piece of bone from mice using Amira2D

Recipe ISP (hxisp,a2d)

3 Jul 2020 - This is a workflow to segment out osteocytes present in mouse bone sample using Amira2D

NEW Porosity and Permeability by blocks

Porosity and Permeability by blocks

Tcl

3 Jul 2020 - Splits a binary pore space into blocks and output one porosity and permeability value for every block

NEW Extracting and Visualizing Local Statistics from Fibrous Materials

Extracting and Visualizing Local Statistics from Fibrous Materials

Project (hx, pgo)

3 Jul 2020 - This XTRA entry discusses the application of the “Spatial Graph Local Statistics” to extract statistical information from traced fibers in a fibrous material. The sample is 50% glass fiber-reinforced polymer (GFRP), courtesy of EMS Grivory.

NEW Interactive Top-Hat by Reconstruction.

Interactive Top-Hat by Reconstruction.

XPand module

3 Jul 2020 - This module provides an interactive Top-Hat segmentation that prevents from segmenting false positive porosity on the edges.

NEW  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

NEW Cell Detection and Tracking 2020.2

Cell Detection and Tracking 2020.2

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

17 Jun 2020 - Simple workflow for tracking cell nuclei in a 3D Time Series.

NEW XFiber Automation

XFiber Automation

Tcl, Project (hx, pgo), Data

17 Jun 2020 - To make use of XFiber, the user usually needs to input many parameters. This package provides 2 tools to ease Xfiber process by presetting Cylinder Correlation and Auto Trace Correlation modules values.

NEW Avizo User's Guide translated to Japanese

Avizo User's Guide translated to Japanese

Demo, Misc

11 May 2020 - You will find here a selection of Avizo tutorials translated to Japanese.

NEW Molar Segmentation Using Watershed and Top-Hat and Surface Generation

Molar Segmentation Using Watershed and Top-Hat and Surface Generation

Project (hx, pgo), Demo, Data

11 May 2020 - Data, tutorial, and complete project for segmenting a CT-scanned human molar artifact. The tutorial and project cover advanced image segmentation and surface generation.

NEW Extract Label

Extract Label

Python (pyscro)

11 May 2020 - This module extracts a specified label region by the ID

Copy Measure Annotation Settings

Copy Measure Annotation Settings

Tcl

15 Apr 2020 - This Tcl script-object can be used to copy visualisation settings from one measure to all others in a Measurement module. It is also possible to save/load settings to/from a text file.

Caption From Port

Caption From Port

Tcl

15 Apr 2020 - Use this module to fill the text field of a Caption module with the value of a port of another module.

Scale-Space Laplacian of Gaussian Filter

Scale-Space Laplacian of Gaussian Filter

Python (pyscro)

15 Apr 2020 - Image processing filter enhancing spherical or blob like objects of various sizes.

Disp View

Disp View

Python (pyscro)

4 Mar 2020 - This module allows the user to visualise a vector field, computed using the Digital Volume Correlation module, with arrows coloured according to the magnitude of the vector.

Cumulate Displacement Field

Cumulate Displacement Field

Python (pyscro)

4 Mar 2020 - This module allows the user to add multiple displacement fields.