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
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. The contours will be manually defined on the chocolate-bar.am.
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
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
Python (pyscro)
22 Jan 2021 - With this Python script-object you can convert a point-cloud object to a spreadsheet object.
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
Multi-Component Analysis of X-ray Computed Tomography Datasets
Recipe (hxrecipe), Project (hx, pgo), Demo, Data, Misc
4 Jan 2021 - The following videos and training material detail the steps taken to automate the analysis of multiple parts in a single X-ray CT volume.
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.
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
Automatic extraction of surface cross section
Python (pyscro), Project (hx, pgo)
20 Oct 2020 - Create partially transparent capping surfaces
Auto Threshold for Multi-Thresholding
Tcl
19 Oct 2020 - The combination of Auto Thresholding and Multi-Thresholding makes it easy to create precise surfaces without additional smoothing, using Generate Surface's smoothing option "Existing Weights".
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.
Explode Surface Animation Script
Tcl
5 Oct 2020 - A script that will animate the expansion of pieces of a surface. Contains the script, documentation, an example surface, and a video of the finished result.
PerGeos Process Based Modelling
XPand module
4 Sep 2020 - Process Based Modelling modules for PerGeos