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 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.

NEW Selective Border Kill

Selective Border Kill

Tcl

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

NEW 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.

NEW 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.

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

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

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 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

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.

Extract Label

Extract Label

Python (pyscro)

11 May 2020 - This module extracts a specified label region by the ID Supports 8, 16 and 32 bit label

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.

Amira User's Guide translated to Japanese

Amira User's Guide translated to Japanese

Demo, Misc

29 Jan 2020 - You will find here a selection of Amira tutorials translated to Japanese.

Create Label Annotations

Create Label Annotations

Tcl

13 Dec 2019 - This module creates label annotations from the result of a Label Analysis with the help of the Measurement tool.

Average interleaved data

Average interleaved data

Python (pyscro), Project (hx, pgo)

21 Oct 2019 - The purpose of this python script object is to average interleaved data.

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)

21 Oct 2019 - This script simply reads and loads numpy arrays in a user specified directory into PerGeos/Amira-Avizo as an image.

Length Distribution Analysis

Length Distribution Analysis

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

21 Oct 2019 - This tutorial demonstrated how to quantify thickness distribution along the length