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.
NEW
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.
NEW
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).
NEW
Tcl
8 Mar 2021 - Script module to fit molecular models to density maps, a process frequently called "docking".
NEW
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.
NEW
Demo, Misc
24 Feb 2021 - This video tutorial demonstrates how to deal with visualization of large datasets.
NEW
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.
NEW
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.
NEW
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.
NEW
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.
NEW
Efficient Graph-based 2D Image Segmentation
XPand module
12 Feb 2021 - This Xtra implements efficient graph-based image segmentation by Felzenszwalb and Huttenlocher.
NEW
Demo
10 Feb 2021 - This tutorial explains how to export a movie file from the Animation Director.
NEW
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.
NEW
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.
How to Create and Animate a Camera Path
Demo
3 Jan 2021 - This short tutorial explains how to create a camera path and then animate the camera along this path with the Animation Director.
How to Animate the Appearance of Objects with the Animation Director
Demo
3 Jan 2021 - This short tutorial explains how to animate the appearance and disappearance of objects with the Animation Director.
How to Get Started with the Animation Director
Demo
3 Jan 2021 - This short tutorial will take you through the basis of animation creation with the Animation Director.
Tcl
17 Nov 2020 - It might be desired to export the measures and annotations created with the Measurement tool of Amira/Avizo for further analysis. This module creates a spreadsheet with the data of the measurements and annotations.
Recipe ISP (hxisp,a2d)
17 Nov 2020 - Recipe for Marker Based Watershed as in the Segmentation Editor