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.
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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 Extract Label

Extract Label

Python (pyscro)

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

NEW 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.

Green-Lagrange Strain

Green-Lagrange Strain

Python (pyscro)

4 Mar 2020 - This module allows the user to compute the Green-Lagrange strain tensor from a displacement field.

Convert To Volume

Convert To Volume

Python (pyscro)

4 Mar 2020 - This module allows the user to re-map a DVC scalar field (displacement and strain components) stored in a mesh into a lattice dataset (image).

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.

Random Forests for Multiclass Segmentation using Python API in PerGeos

Random Forests for Multiclass Segmentation using Python API in PerGeos

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

21 Oct 2019 - Simple demonstration of feature computation where the feature vector contains intensity and 2D eigenvalues (X & Y). This example uses random forests implementation from the sklearn package.

Depthwise Volume Fraction

Depthwise Volume Fraction

Python (pyscro)

17 Oct 2019 - This module allows the user to compute the volume fraction per separated region depending on depth from the surface of a segmented object.

Parameter optimization for auto-thresholding a data

Parameter optimization for auto-thresholding a data

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

7 Oct 2019 - In this pyscro example we use opencv and matplotlib to automatically calculate an optimized parameter for thresholding the data based on various metrics.

How to use PyQt5 in a pyscro module

How to use PyQt5 in a pyscro module

Python (pyscro)

7 Oct 2019 - This example shows how to use PyQt5 in a pyscro module.

Convert To Spreadsheet

Convert To Spreadsheet

Python (pyscro)

3 Oct 2019 - This module allows the user to convert a scalar/vector/tensor field into a spreadsheet containing the X,Y,Z positions and the values of the field.

Scalar Extract

Scalar Extract

Python (pyscro)

3 Oct 2019 - This module extracts the displacement and strain components computed using the Digital Volume Correlation module.

Incremental Global DVC

Incremental Global DVC

Python (pyscro)

3 Oct 2019 - Perform incremental DVC analysis for a series of deformed image, using either small strain or large strain approaches (note: to run correctly the Green Lagrange strain script needs to be installed).

DVC Accuracy

DVC Accuracy

Python (pyscro)

3 Oct 2019 - This module allows the user to measure the displacement and strain errors from two repeat scans.

Particles identification in Nickel-Base Superalloy

Particles identification in Nickel-Base Superalloy

Recipe ISP (hxisp,a2d), Python (pyscro), Data

24 Jul 2019 - FIB Serial Section of Particles in Nickel-Base Superalloy

Automated sizing of large area nanoparticles

Automated sizing of large area nanoparticles

Recipe ISP (hxisp,a2d), Python (pyscro)

25 Jun 2019 - The recipe segments large area Pt-Rh nanoparticles at high resolution (TEM image).