Amira-Avizo Software Revamped Documentation New
How-to

Amira-Avizo Software Revamped Documentation

Demo

1 Aug 2024 - This short video provides an overview of the changes we have made to improve the accessibility of the documentation for the Amira and Avizo Software.  Learn more

Segmentation+ Workroom Tutorial
How-to

Segmentation+ Workroom Tutorial

Demo

2 May 2024 - Discover the Segmentation+ workroom, a powerful tool for interactive 3D image segmentation. This tutorial offers a comprehensive overview of the segmentation process, covering essential principles and tools.  Learn more

How to Use the Arithmetic Module
How-to

How to Use the Arithmetic Module

Demo

2 Jan 2024 - This series of video tutorials introduces the Arithmetic module and examples of use cases.  Learn more

Trabecular Segmentation Workflow for Murine Tibial Bone
Add-on How-to

Trabecular Segmentation Workflow for Murine Tibial Bone

Recipe (hxrecipe), Project (hx, pgo), Demo, Data

11 Dec 2023 - Here we provide a workflow to easily obtain the segmentation of trabecular bones.  Learn more

Visualize Identified Molecules of a Cryo-Tomogram
Add-on How-to

Visualize Identified Molecules of a Cryo-Tomogram

Python (pyscro), Project (hx, pgo)

4 Dec 2023 - This Xtra provides the means to import results from template matching and visualize them with the Molecule Cloud View module. In addition, a module is provided to crop point clouds according to an ROI-box.  Learn more

Visualization Templates
Add-on

Visualization Templates

Python (pyscro)

11 Sep 2023 - A set of four templates to create rapid and efficient visualization of your data  Learn more

Python Command Module
Add-on

Python Command Module

Python (pyscro)

6 Mar 2023 - A module to enter and execute Python code from Amira-Avizo Software interface.  Learn more

AI Assisted Tool for CryoEM Segmentation
How-to

AI Assisted Tool for CryoEM Segmentation

Demo, Data

28 Nov 2022 - Here we provide a tutorial to interactively segment a cellular cryo-electron tomography image using the AI assisted segmentation tool of the Segmentation+ workroom.  Learn more

Iterate Recipe
Add-on

Iterate Recipe

Python (pyscro)

17 Nov 2022 - This module allows you to run a given recipe while varying a chosen parameter value of any of the modules making up the recipe.  Learn more

Surface Material Grid View
Add-on

Surface Material Grid View

Tcl

18 Oct 2022 - This Xtra arranges all materials of a surface in a grid view.  Learn more

Eval on Spatial Graph
Add-on

Eval on Spatial Graph

XPand module

8 Sep 2022 - This Xtra provides a module that evaluates a scalar field at each point of a Spatial Graph and stores the result as the thickness attribute of the resulting Spatial Graph.  Learn more

Volume Operations: Flip, Swap, Auto-Crop, and Enlarge
Add-on

Volume Operations: Flip, Swap, Auto-Crop, and Enlarge

XPand module

8 Sep 2022 - This Xtra contains a set of modules that allow you to perform and automate volume operations on your data.  Learn more

Extract Objects
Add-on

Extract Objects

XPand module

1 Sep 2022 - The Xtra module extracts single objects based on label information listed in a Label Analysis.  Learn more

Reconstruct Spatial Graph from Markers
Add-on

Reconstruct Spatial Graph from Markers

XPand module

1 Sep 2022 - This Xtra filters a Spatial Graph to keep only segments that have at least one point in each of the labels of an input Label Field.  Learn more

Divide Full Data Volume into Defined Sub-Volume Blocks for Label Analysis
Add-on How-to

Divide Full Data Volume into Defined Sub-Volume Blocks for Label Analysis

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

1 Sep 2022 - This Xtra demonstrates how to use the Arithmetic module to divide a whole volume data into defined sub-volume blocks and then perform label analysis on the blocks.  Learn more

How to Install the Deep Learning Python Environment
How-to

How to Install the Deep Learning Python Environment

Python (pyscro), Demo, Misc

29 Jul 2022 - Two videos explain how to install the dependencies needed to use Deep Learning within Amira 3D, Avizo 3D, or Pergeos. One covers the standard install and the other is for users without an internet connection.  Learn more

How to Calculate Surface Area of a Custom ROI
How-to

How to Calculate Surface Area of a Custom ROI

Demo, Data

29 Jul 2022 - This tutorial elaborates how to draw a region of interest on a surface. With this ROI, you can calculate its surface area.  Learn more

How to Calculate Surface Area
How-to

How to Calculate Surface Area

Demo

29 Jul 2022 - Three approaches are shown for extracting a surface and measuring the surface area of its geometry.  Learn more

Plane Tools - Surface and Volume Distance to Plane and Spatial Graph Projection onto Plane
Add-on

Plane Tools - Surface and Volume Distance to Plane and Spatial Graph Projection onto Plane

XPand module

26 Jul 2022 - This Xtra provides a set of three modules to compute distance and projection to a user-defined plane.  Learn more

Xtras Installer for Amira-Avizo 2023.1 and Prior
Add-on

Xtras Installer for Amira-Avizo 2023.1 and Prior

Recipe (hxrecipe), Recipe ISP, IVP, A2D, Deep learning model, Python (pyscro), Tcl, XPand module, Project (hx, pgo), Template, Demo, Data, Misc

30 Jun 2022 - The Xtras Installer is a tool that provides an easy way to install resources from the Xtra Library on to your local machine.  Learn more

Image Stack Builder
Add-on

Image Stack Builder

Python (pyscro)

10 Jun 2022 - This module merges together a set of several 2D/3D images into one single volume. It is very helpful for building a 2D image stack from a set of 2D images for ground truth definition.  Learn more