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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How to Script the Instantiation of a Python Script Object Xtra NEW
Add-on How-to

How to Script the Instantiation of a Python Script Object Xtra

Python (pyscro)

9 Sep 2021 - This Xtra provides a script template that can be used to instantiate a Python script object Xtra from the Python console or from a Python script.

Browse TensorBoard of old Deep Learning Training sessions
Add-on

Browse TensorBoard of old Deep Learning Training sessions

Deep learning model, Python (pyscro)

21 May 2021 - This Xtra proposes a module allowing you to browse TensorBoard logs from previous Deep Learning Training sessions.

Add Data To Point Cloud
Add-on

Add Data To Point Cloud

Python (pyscro)

29 Mar 2021 - AddDataToPointCloud writes data defined on mesh-nodes into a point-cloud with equal number of points. Together with the Xtra "PointCloudToSpreadsheet", the module can e.g. be used to export the results created by the module Surface Distance.

Extract Oriented Labels
Add-on How-to

Extract Oriented Labels

Python (pyscro), Project (hx, pgo)

29 Mar 2021 - The Extract Oriented Labels module extracts every label from the input label image, and resamples each image along its own main orientations (or eigenvectors).

Image Segmentation Evaluation Using Standard Metrics (Python)
Add-on

Image Segmentation Evaluation Using Standard Metrics (Python)

Python (pyscro), Project (hx, pgo)

8 Mar 2021 - Segmentation evaluation using standard precision, recall metrics for comparing two segmentation labels.

Patch Extraction Tools for Deep Learning data preparation
Add-on

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
Add-on

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.

Point Cloud to Spreadsheet
Add-on

Point Cloud to Spreadsheet

Python (pyscro)

22 Jan 2021 - With this Python script-object you can convert a point-cloud object to a spreadsheet object.

Thresholding From Mean
Add-on How-to

Thresholding From Mean

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
Add-on

Automatic extraction of surface cross section

Python (pyscro), Project (hx, pgo)

20 Oct 2020 - Create partially transparent capping surfaces

Volume Projection
Add-on

Volume Projection

Python (pyscro)

19 Oct 2020 - Volume projection along any orthogonal axis using arithmetic operations.

Relative Area Fraction for Amira-Avizo2D
Add-on How-to

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
Add-on How-to

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.

Hough Circle Fitting
Add-on

Hough Circle Fitting

Python (pyscro)

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

Multi-Scale Cylinder Correlation
Add-on How-to

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
Add-on

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.

Extract Label
Add-on

Extract Label

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
Add-on

Scale-Space Laplacian of Gaussian Filter

Python (pyscro)

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

Average interleaved data
Add-on

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
Add-on

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
Add-on

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.