How to Install the Deep Learning Python Environment New
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 New
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 New
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 New
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

Image Stack Builder New
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

Object Separation using Random-Walk Distance Map New
Add-on

Object Separation using Random-Walk Distance Map

Recipe ISP, IVP, A2D, Demo, Data

3 Jun 2022 - Recipe realizing an object separation workflow relying on Random-Walk Distance Map. It is more robust to noisy segmentation or non-spherical shapes, compared to Separate Object.  Learn more

Create Material IDs New
Add-on

Create Material IDs

Tcl

1 Jun 2022 - Using this module, the "Materials" parameter-bundle of a label-field is created and filled with an ID and name for each label-value.  Learn more

Scientific Scalebar New
Add-on

Scientific Scalebar

Python (pyscro)

13 May 2022 - This Xtra automatically sets the scalebar parameters to comply with the requirements for scientific papers.  Learn more

Scale Axes New
Add-on

Scale Axes

Tcl

13 May 2022 - The coordinate-axes displayed using the "Axes" module cannot be scaled easily. Using this Xtra, you can easily change the lengths of the axes and the location of the displayed origin.  Learn more

High Content Screening Plate Manager New
Add-on

High Content Screening Plate Manager

Python (pyscro), Tcl

13 May 2022 - Load, visualize, and process multi-channel fields from Thermo Scientific CellInsight CX5, CX7 LED, and CX7 LZR HCA instruments and HCS Studio software.  Learn more

Bone Segmentation Workflow for Murine Hindpaw
Add-on How-to

Bone Segmentation Workflow for Murine Hindpaw

Recipe ISP, IVP, A2D, Demo, Data

28 Apr 2022 - Semi-automatic workflow and recipe for high-throughput bone segmentation of murine hindpaw micro-CT datasets.  Learn more

Extract Color Wash Image
Add-on

Extract Color Wash Image

Python (pyscro)

28 Apr 2022 - This module exports an image of color-washed data.  Learn more

How to Segment Cavities Using the Compute Ambient Occlusion Module
How-to

How to Segment Cavities Using the Compute Ambient Occlusion Module

Demo

12 Apr 2022 - This tutorial demonstrates how to segment pores or cavities using the Compute Ambient Occlusion module.  Learn more

How to Perform Trabecular and Cortical Bone Segmentation
How-to

How to Perform Trabecular and Cortical Bone Segmentation

Demo

12 Apr 2022 - This tutorial demonstrates how to use the Compute Ambient Occlusion module to perform the segmentation of trabecular and cortical bone, as well as of the pore space, and then how to use the Arithmetic module to aggregate those results in one label field.  Learn more

Slice by Slice Thinning
Add-on

Slice by Slice Thinning

XPand module

6 Apr 2022 - This module performs the thinning of a binary image slice-by-slice.  Learn more

Slab View
Add-on How-to

Slab View

Python (pyscro), Project (hx, pgo)

24 Feb 2022 - The Slab View display module allows you to display only a slab from any kind of 3D visualization.  Learn more

How to Use the Surface View Module and Create Elaborate Surface Renderings
How-to

How to Use the Surface View Module and Create Elaborate Surface Renderings

Demo

30 Dec 2021 - This short video demonstrates the basic use of the Surface View module, and how to combine several Surface View modules to create elaborate renderings.  Learn more

Facies Classification from Well Logs
Add-on How-to

Facies Classification from Well Logs

Python (pyscro), Demo

3 Dec 2021 - Facies (rock type) classification from well logs using supervised machine learning algorithms.  Learn more

How to Customize Amira-Avizo with moduleExtender
Add-on How-to

How to Customize Amira-Avizo with moduleExtender

Tcl, Misc

25 Nov 2021 - Are there module settings you always need to change during your daily work? This Xtra describes how you can permanently change default settings of modules in Amira-Avizo.  Learn more

Masking Map by Molecule
Add-on

Masking Map by Molecule

Tcl

18 Nov 2021 - Module Mask Map By Molecule lets you mask an EM map of a macro molecule by an atomic model of the entire or partial molecule. This can be useful when validating EM maps from SPA with published models from the Protein Data Bank.  Learn more

kMeans Clustering on Label Analysis (Python)
Add-on

kMeans Clustering on Label Analysis (Python)

Python (pyscro)

18 Nov 2021 - This Xtra implements kMeans clustering on a label analysis spreadsheet. Separated objects can be clustered based on any measure group that is inbuilt or user customized.  Learn more