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.

Browse TensorBoard of old Deep Learning Training sessions NEW
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 - This module extracts each single label from the input label image and resamples each of it 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.

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.

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.

Depthwise Volume Fraction
Add-on

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
Add-on

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
Add-on

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
Add-on

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.