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.
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Data
8 Jul 2021 - Data used in the tutorials of Xplore5D extension, available from Amira-Avizo 2021.1
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XPand module
29 Jun 2021 - This module merges the two most representative segments at the intersection points of a graph structure and detaches the others.
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More Resources on Amira-Avizo Learning Center YouTube Playlist
Demo, Misc
4 Jun 2021 - This Xtra provides links to Amira-Avizo Learning Center YouTube playlist.
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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.
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.
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).
Tcl
8 Mar 2021 - Script module to fit molecular models to density maps, a process frequently called "docking".
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.
Getting Started with Flatten module
Project (hx, pgo), Demo
8 Mar 2021 - Get started with the Flatten experimental module. You will learn how to create interactive contours by defining the unfolding surface while respecting the constraints of the module inputs.
Demo, Misc
24 Feb 2021 - This video tutorial demonstrates how to deal with visualization of large datasets.
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.
How to Set Up Two-Sided Clipping
Demo
15 Feb 2021 - This short tutorial explains how to set up two-sided clipping in order to transition between two visualization of data.
How to Use Camera Orbit and Animate a Rotation
Demo
15 Feb 2021 - This short tutorial explains how to use the Camera Orbit module and then animate the rotation around an object in the Animation Director.
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.
Efficient Graph-based 2D Image Segmentation
XPand module
12 Feb 2021 - This Xtra implements efficient graph-based image segmentation by Felzenszwalb and Huttenlocher.
Demo
10 Feb 2021 - This tutorial explains how to export a movie file from the Animation Director.
How to Compare Slices Side by Side
Demo
10 Feb 2021 - This short tutorial explains how to compare side by side two slices displaying different information, for example of raw data and its corresponding labeled image.
Python (pyscro)
22 Jan 2021 - With this Python script-object you can convert a point-cloud object to a spreadsheet object.
Non-Standard Python Package Installation Tutorial
Demo, Misc
13 Jan 2021 - Brief video explaining how to install a Python package in a newly created Python environment using pip or edm.
FIBSEM Mitochondria Segmentation
Deep learning model
12 Jan 2021 - Pre-trained model for the Deep Learning Prediction module detecting mitochondria in a Focused Ion Beam Scanning Electron Microscope (FIBSEM) data set
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.