Bruker-MicroCT method note: 3D visualization of …€¦ · Page 2 of 18 2 Bruker-MicroCT method...

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3D visualization of open

and closed porosity

Method note

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2 Bruker-MicroCT method note: 3D visualization of open and closed porosity

Introduction

The goal of this application note is to evaluate the porosity of a specific object. As an

illustration for this application note, a rock was scanned and analyzed (‘Rock subsea’

dataset). Looking to the reconstructed images of the sample, one can see that the

rock has a porous structure (see image below). The first part of this application note

will illustrate how to quantify the general porosity, as well as the open and closed

porosity of a sample. The second part will focus on how to generate a visual 3D

representation of the porosity, and distinguish between open and closed pores.

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Before you start…

Before opening a dataset in

CTAn, select the right

nomenclature settings for

your type of application in

the File > Preferences

window. One has the choice

between either ‘General

scientific’ or ‘Bone ASBMR’

nomenclature. For the rock,

‘General scientific’

nomenclature was selected.

The unit was set to

millimeter.

By clicking the ‘Open dataset’ buttom, one can browse to the reconstructed images

of the sample to be analyzed. Note that when the dataset dimensions are too large to

be processed by the computer, the dataset can be resized by ticking the ‘resize by’

box and specifying an appropriate resizing factor.

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Part 1: Regions of interest page

Upon opening of the dataset in CTAn, immediately browse to the ‘Regions

of interest’ page.

Analysis of the porosity of the rock requires an appropriate region of interest (ROI) to

be selected. Without a region of interest, the porosity will be calculated relative to the

volume of the total dataset, including the air surrounding the sample, which would

give an overestimation of the porosity, pore volume, etc. Depending on the sample or

application, one has the choice between either several geometrical shapes or a

freehand selection as region of interest. By clicking the ROI dimensions, one has the

possibility to predefine exactly the dimensions of the ROI if wanted. In this case, a

circular region of interest with a diameter of 5 mm was selected completely within the

rock.

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In a next step, also the top and bottom of the region of interest (in the Z-direction)

have to be specified. To do so, right click the slices to be determined as the top and

bottom of the region of interest and select ‘Set top of selection’ or ‘Set bottom of

selection’, respectively.

Note that one can also save this region of interest by clicking the ‘save ROI’

button. This option is required to process multiple datasets in batch mode

using CTAn Batch manager.

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Part 2: Binary images page

Once an appropriate region of interest (in 3D called volume of interest or

VOI) is selected, one can proceed to the ‘Binary images’ page.

In the ‘Binary images’ page, an appropriate threshold has to be chosen to select

certain structures based on the grey values. Setting the right threshold can be done

either by shifting between and comparing the raw image (press ALT+1) and the

binary image (press ALT+3), or by setting the threshold using the ‘Toggle halftone

view’ function.

In this case, the rock material is selected by putting a threshold from 60 to 255.

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Part 3: Custom processing page

Once the appropriate threshold values are selected, proceed to the ‘Custom

processing’ page.

A copy of the dataset will be loaded. Three very important buttons are on the right

side of the plug-ins bar:

image view

image inside ROI view

ROI view

As you have just loaded a copy of the dataset into the custom processing page, the

initial settings are:

Image view Image inside ROI view ROI view

In order to calculate the porosity of the rock within the volume of interest, one has to

first threshold the image. Run the thresholding plug-in (global) using the selected

values (60-255 in this case). Note that when you select the ‘default’ option, CTAn will

upload the values that you have selected last in the binary page.

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Due to noise, certain pixels can be thresholded and appear as white dots or

speckles. Therefore, the next step is to run a despeckling function, removing white

speckles in 3D that are smaller than 10 voxels. Note that this preset has to be

optimized according to every individual application or sample type, based on the size

of the white speckles. The same despeckling procedure can be performed to remove

black speckles (‘remove black speckles’), depending on the sample and tresholding

result.

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Following the despeckling step, the 3D analysis plug in can be run to calculate the

porosity of the sample within the volume of interest. One can chose the option to

save the results as a single line to a .csv file, which is particularly useful when

running a batch mode analysis. Note that with the same plug-in, several other

parameters can be calculated including object volume, structure thickness, structure

separation, etc.

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Part 4: Data analysis

To analyze the data, import the .csv file into excel. One can see that different

parameters can be used to describe the porosity of a sample; number of pores,

volume of pores, surface of pores and percentage of pores. In addition, the pore

analysis is subdivided in total pores, closed pores and open pores (see table below).

An accurate study of a sample’s porosity requires correct understanding of the

definition of the parameters ‘open pore’ and ‘closed pore’, and how they are

calculated.

An ‘open pore’ or ‘broken pore’ is a pore intersecting the boundary of the volume of

interest, or in other words a pore that is connected to the outside in 2D or 3D.

Therefore open pores are classified as a property of the VOI. A ‘closed pore’ in

contrast is a pore that is not connected to the outside in 2D or 3D, or in other words a

group of black pixels that is fully surrounded by a border of white pixels.

Subsequently, closed pores are classified as a property of the material itself. As a

consequence, open and closed porosity are not calculated in the same way.

The total porosity is calculated as the volume of all pores (open and closed pores) as

a percent of the total of solid plus pore (open and closed) volume within the VOI

(which thus equals the VOI volume). Note that this parameter can also be calculated

from the percent object volume parameter. In analogy, the open porosity (a VOI

property) corresponds to the volume of open pores as a percentage of the total VOI

volume. However, as closed porosity is a material property, closed porosity is

calculated as the volume of closed pores as a percentage of the total material

volume, being defined as the total VOI volume without the open pore volume or in

other words the material volume including the closed pore volume (object volume

plus closed pore volume). Therefore, note that the percent total porosity not always

equals the sum of the percent open porosity and the percent closed porosity. In this

case, the total porosity is 9.11%, the open porosity 5.09% and the closed porosity

4.23%.

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Description Abbreviation Value Unit

Total VOI volume TV 44.88 mm^3

Object volume Obj.V 40.79 mm^3

Percent object volume Obj.V/TV 90.89 %

Number of closed pores Po.N(cl) 4515.00

Volume of closed pores Po.V(cl) 1.80 mm^3

Surface of closed pores Po.S(cl) 157.43 mm^2

Closed porosity (percent) Po(cl) 4.23 %

Volume of open pore space Po.V(op) 2.29 mm^3

Open porosity (percent) Po(op) 5.09 %

Total volume of pore space Po.V(tot) 4.09 mm^3

Total porosity (percent) Po(tot) 9.11 %

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Part 4: Visual 3D representation of open and closed pore distribution

This section will focus on how to create a 3D model of the sample, allowing the visual

inspection of the open and closed pore distribution separately in the SkyScan CTVol

software. In fact, 3 3D models will be generated; a 3D model of the total VOI

including both the rock (solid) material and the pores, a 3D model of the closed pores

only and a 3D model of the open pores only. As such, one will be able to assign

different colors to the different models in CTVol. Note that this application is not

possible by volume rendering software (CTVox) as all pores have the same density

and can thus not be visualized in different colors. There certainly are several ways to

perform this analysis in CTAn. In this application note, one procedure will be

described step by step that can also be performed in a fully automated way using the

batch manager in CTAn.

One can continue with the result obtained by the thresholding and despeckling steps

described before in part 3 of this application note. The first step now is to generate

the 3D model of the VOI. Run the ‘3D model’ plug-in and apply to the ROI.

Next, run a bitwise operation to limit the image to the region of interest.

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To generate a 3D model of either the closed pores or the open pores, one has to

eliminate one type of pores from the image in the next step. In this case, all open

pores (thus pores that are connected to the outside) were removed by running a

despeckling function removing ‘broken pores’ in 3D detected by ROI borders.

The result is an image in which both the rock material as well as the open pores are

selected, leaving only the closed pores deselected.


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To make a 3D model of the pores, in this case closed pores, invert the image by

running the bitwise operation ‘image = NOT image’.

The result is an image in which only the closed pores are selected within the VOI.


Run the ‘3D model’ plugin and apply it to the image inside the ROI to create a 3D

model from all closed pores.

So far, a 3D model was created for the total VOI, and for all closed pores. In the last

part, a 3D model will be created from all open pores. Therefore, all closed pores have

to be excluded from the VOI. To do so, run a bitwise operation to limit the ROI from

the original ROI to a new ROI including the rock material itself as well as the open

pores and excluding the closed pores. Note that the image inside ROI view is now

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empty as the closed pores selected in the image view are not selected anymore in

the ROI view.


Selection of the open pores requires reloading the image.


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Again, run the tresholding and despeckling steps to select the rock material as

described before in part 3. Note that the image inside ROI view looks exactly the

same as the image obtained in part 3, showing both open and closed pores. Yet, the

closed pores are not selected in the VOI.


Analogeously to the selection of the closed pores, select the open pores by inverting

the image. Run the bitwise operation ‘image = NOT image’. By this step, it also

becomes more clear (visually) from the image inside ROI view that only the open

pores are selected in this step.

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The last step is now to run the ‘3D model plug-in, applying it to the image inside ROI

to create a 3D model for all open pores.

Open all 3 3D models in the SkyScan CTVol software, and assign different colors to

the different models. In this case, blue was selected for the total volume of interest,

red was selected for the open pore model and green for the closed pore model. In

addition, the volume of interest model was set transparent (opacity 40%) as well as

the pore models (opacity 60%), giving a better representation of the pores inside the

volume of interest (image 1). One might prefer other representations as well, for

example showing only the open pores in one side of the rock and the closed pores in

the other side (image 2), or cutting the complete model in half and look from the

inside (image 3). To do so, the corresponding models can be cut by the plane which

can be selected from the list of 3D models in the objects window.

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Image 1

Image 2

Image 3

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