3D image analysis and visualisation modules for Avizo

(latest version : 0.93, November 30^th, 2023)

 

As a by-product of several years of study and research on the use of X-ray CT (tomography) imagery for material characterisation, a set of 3D image processing and analysis modules have been developed and integrated in Avizo, which you can download freely as an installer package.

 

The package contains compute and visualisation modules ranging from basic morphological filters to more elaborate operators taylored for a specific problem. All modules defined in this package are either found in an EP/ subdirectory in Avizo, or are prefixed by "EP_". The modules should all be documented, and in each help file is a link to the list of all modules in this package.

 

The latest integration is made in Avizo 9.2 for Windows.

 

The complete list of modules in this package is presented here, with links to all related documentation.

Notes

• These modules were previously available in the Image Quantification Algorithms project on CCPForge, which unfortunately has closed.
• If you make use of these modules please acknowledge Erwan and the sources of the algorithms as listed in the corresponding help files.
• If you would like these modules updated for a more recent version of Avizo, please let me know.

 

Examples

Here are a few examples of modules found in the package.

Watershed

 

Separates connected regions or objects in an image. Needs some pre-processing to seed the regions and define a topography to guide the segmentation (e.g. using a distance transfom).

 

Visualisation of object separating surfaces

After segmentation, shows the voxel faces that are shared between two regions.

Geodesic distance

 

Distance inside an object or a mask. Useful for measures of tortuosity.

Vector field visualisation

Shows in 3D a vector field, with several option to improve the clarity.

Particle tracing

Given a vector field representing a flow, simulates massless particles inside, with measures such as speed, particle age, constraints accumulated, etc.

 

Rose diagram

Used on the autocorrelation function, produces a measure of anisotropy.

Distance histogram

 One possible measure of the size of structures. The most these are big or thick, the more the histogram with be spread towards the right (higher distances to the structre edges).

 

Random sphere packings

 

To simulate model materials, generates random sphere packings (quasi-compact or not), along with 3D images of any resolution, the 3D scene, and the adjacency graph.

Side identification

For cuboids, identifies the 6 sides supposing they're aligned with the image grid. Useful for filtration calculations.

Partition to graph conversion

Linked to transport phenomena, generates from a segmented image a graph structure.