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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Patch Extraction Tools for Deep Learning data preparation
Python (pyscro)
22 Feb 2021 - A set of tools dedicated to preparation of data for training Deep Learning models and reducing annotation time.
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.
Python (pyscro)
22 Jan 2021 - With this Python script-object you can convert a point-cloud object to a spreadsheet object.
Python (pyscro), Data
4 Jan 2021 - This module performs an adaptive global thresholding of the input image by computing a deviation from the mean of its grayscale values.
Automatic extraction of surface cross section
Python (pyscro), Project (hx, pgo)
20 Oct 2020 - Create partially transparent capping surfaces
Python (pyscro)
19 Oct 2020 - Volume projection along any orthogonal axis using arithmetic operations.
Relative Area Fraction for Amira-Avizo2D
Recipe ISP (hxisp,a2d), Python (pyscro), Data, Misc
5 Oct 2020 - This Xtra provides a module to help compute the area fraction of a label over the area of another label in Amira-Avizo2D.
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.
Python (pyscro)
30 Jul 2020 - Generalized Hough transform to fit circles to the image.
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.
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.
Python (pyscro)
11 May 2020 - This module extracts a specified label region by the ID Supports 8, 16 and 32 bit label
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.