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.
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.
Python (pyscro)
11 May 2020 - This module extracts a specified label region by the ID
Scale-Space Laplacian of Gaussian Filter
Python (pyscro)
15 Apr 2020 - Image processing filter enhancing spherical or blob like objects of various sizes.
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.
Python (pyscro)
4 Mar 2020 - This module allows the user to add multiple displacement fields.
Python (pyscro)
4 Mar 2020 - This module allows the user to compute the Green-Lagrange strain tensor from a displacement field.
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).
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
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
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.
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
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
Python (pyscro)
7 Oct 2019 - This example shows how to use PyQt5 in a pyscro module.
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.
Python (pyscro)
3 Oct 2019 - This module extracts the displacement and strain components computed using the Digital Volume Correlation module.
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).
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
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
Recipe ISP (hxisp,a2d), Python (pyscro)
25 Jun 2019 - The recipe segments large area Pt-Rh nanoparticles at high resolution (TEM image).