Rock sample porous network analysis By Visualization ......Avizo Wind Edition capability can be used...

1 http://www.vsg3d.com/vsg_prod_avizo_overview.php Copyright VSG 2009

Rock sample porous network analysis By Visualization Sciences Group, Inc.

Avizo Fire and Wind Editions http://www.vsg3d.com/vsg_prod_avizo_overview.php

Avizo Fire® is an advanced 3D visualization and analysis software application for exploring and analyzing rock samples. From straightforward visualization and measurement to advanced image processing, quantification and skeletonization, Avizo Fire delivers an extensive set of tools addressing 2D and 3D visualisation, rock characterization, reconstruction of 3D rock models and pore networks analysis. In this case study we want to analyse a rock sample acquired through FIB/SEM. The data consists of 355 slices, each slice being a TIF 8 bit encoded file with a 3072 x 2304 resolution. The actual voxel size is 2.8x2.8x5 nm anisotropic. The total size of the data on disk is 2.34GB. This data can be loaded in main memory running on a 64 bit system such as Windows XP/Vista 64 or Linux 64 flavor. On a 32 bit system, the data will need to be loaded as “out-of-core” data using the Avizo XLVolume capability and the Large Data Access technology. It is to notice that Avizo can load byte, signed and unsigned short, sign and unsigned int as well as float, double and complex encoding data. Avizo provides a wide range of standard readers including all standard image formats and also Dicom support as well as raw data import. Using LDA allows for pre-processing of data in a hierarchical multi-resolution structure, that is compressed resulting in a smaller foot print on disk. LDA data can then be loaded on demand and whole data can be visualize (at sub-resolution according to memory constraints). Some algorithms require data to be in-situ in order to operate, such as segmentation, thus a region of interest (ROI) can be defined to load in memory a sub part of the whole data at full or sub resolution. This ROI residing in memory, the in-situ algorithms can apply. The data are loaded either way. When loading a stack of images, the unit and size information are usually not available, thus Avizo is prompting the user to enter information about the voxel size for instance and in case of multi-channel images, asking how to load these channels. In this case we know the voxel size is 2.8x2.8x5 nm anisotropic and we want to load unique channel1, the image being a gray scale. We can perform our first visualization using a VoltexHighQuality module, using latest shading techniques and producing high quality lighted volume rendering of the whole data set so we can have a first look at our rock sample:


The sample data set maybe actually tilted according to camera direction. Avizo provides a Shear correction module that can be used to reorient the slices according to camera direction by shearing the volume according to a specific angle:

Pore

Organic

Mineral


During the acquisition process small image drift can happen due to acquisition process itself or due to environment vibration for instance. This is the case for our sample so slices are not perfectly aligned. This can be seen with the jiggering effect in the XY plane, looking at the stack from the top for instance:

The compute AlignSlices module can be used to automatically re-align the stack using a least square algorithm based on image intensity. Once the stack is aligned we crop the data set to remove jiggering borders:


A ROI can be defined, so we can get a higher resolution of a smaller part if necessary:

Different color maps can be applied with transparency map:


Clipping plane can be activated to see inside the volume (multiple clipping planes can be applied to all of the visualization modules):

Different slicing techniques can be used and combined such as orthogonal slice, oblique slice with whatever orientation, or curved slices:


Isosurface, the surface representing all of the voxels with a given threshold can also be extracted:

Basic image measurement and statistics includes intensity histogram, correlation plot, point and line probe in 2D and 3D, length, angle and radius measurement in 2D and 3D. Notice that measure are according to the unit that was given when dataset was loaded. In this case we know we gave nm, so measurement are given using this unit, nm for length, nm^2 for area and nm^3 for volume:


A variety of 2D/3D image filters can be applied to remove noise or enhance features:

3D surface can be reconstructed through the segmentation editor. The segmentation editor provides the user from manual tools to fully automatic extraction based on threshold. A wide range of semi-automatic tools allows for even faster selection of regions to be assigned to a specific material. Selection interpolation, region growing, snakes are provided for efficient segmentation. (Notice that for the purpose of this use case, following is done on a crop region of the initial data).


Solid Organic Pores

Different computations can be applied to a surface in Avizo and acquired or computed color field can be applied to surfaces, for instance surface curvature:


From the segmented materials, 3D surfaces can be reconstructed, simplified, cleaned-up and 3D volumetric meshes can be generated to be exported for FEA/CFD analysis. The solution can be then imported in Avizo for post-processing to look at stress displacement for instance or flow behavior. The initial surface in this case is made of over 28 millions triangles for the 3 phases that has been identified. Much too complex for both purpose of visualization and mesh generation. The surface is here simplified to just over 200K triangles:


After segmentation, some statistical information can be retrieved using MaterialStatistics module onto the materials (labelField):


Avizo Wind Edition capability can be used in conjunction with Avizo Fire to collaborate with simulation solutions. The 3D grid can be exported to a simulation solver for flow or stress analysis for instance. In this case a simple flow simulation was ran and results were brought back in Avizo Wind to perform post-processing and flow analysis:


We are interested in quantifying the porous structure inside the material. For this purpose Avizo Fire Edition provides the user with advanced quantification capability that allows for pore structure analysis. Mainly based on binarisation and separation through watershed algorithms, including high end 2D and 3D filters, complex statistical analysis can be performed easily. Here we are quantifying the pores in the material:

Skeletonization techniques provided by Avizo can reconstruct pore network for in-depth connectivity analysis to predict petro physical properties of rocks for instance:


Various measures can be computed using Avizo Fire Edition. Here are computed volume, equi-diameter as well as bounding box ratio for each of the pores:


Other standard measures for each pore are also computed, such as moment of inertia for instance:

Pores distributions according to each of the measure can be also computed:


All of the visualization modules can be combined. High quality snapshots at poster quality can be generated and complex and compelling animation can be created and exported to movie format such as MPEG or AVI. Avizo also support stereo viewing for even greater 3D experience and from simple single screen configurations to high end immersive environment.

Rock sample porous network analysis By Visualization ......Avizo Wind Edition capability can be used...

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