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 High Content Screening Plate Manager

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.

Export Measures

Export Measures

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.

Auto Threshold for Multi-Thresholding

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".

Apply a Recipe on a Batch of Files

Apply a Recipe on a Batch of Files

Recipe (hxrecipe), Tcl

25 Aug 2020 - Apply a recipe to a batch of files and save results in output directory.

Selective Border Kill

Selective Border Kill

Tcl

24 Aug 2020 - Filter particles based on their contact with each border of the image

Segment TEM data without artifact  and background effect

Segment TEM data without artifact and background effect

Recipe (hxrecipe), Tcl, Project (hx, pgo)

10 Jul 2020 - Segment TEM data aided by the Structure enhancement filter.

Copy Measure Annotation Settings

Copy Measure Annotation Settings

Tcl

15 Apr 2020 - This Tcl script-object can be used to copy visualisation settings from one measure to all others in a Measurement module. It is also possible to save/load settings to/from a text file.

Caption From Port

Caption From Port

Tcl

15 Apr 2020 - Use this module to fill the text field of a Caption module with the value of a port of another module.

Create Label Annotations

Create Label Annotations

Tcl

13 Dec 2019 - This module creates label annotations from the result of a Label Analysis with the help of the Measurement tool.

Auto-Crop script module

Auto-Crop script module

Tcl

16 Oct 2019 - Automatically crop your volume data to reduce its size.

Export Spatial Graph to MS Excel XML document

Export Spatial Graph to MS Excel XML document

Recipe (hxrecipe), Tcl, Demo

16 Oct 2019 - An Amira-Avizo recipe to export to a XML document which can be used in MS Excel for further analysis.

View Manager

View Manager

Tcl

14 Oct 2019 - This module allows storing and retrieving camera settings for viewer windows to be able to switch easily between different view presets.