How to Identify Pore-Geophysical parameters of 2D_Thinsection_Sandstone Image by Image Processing

@Shubham_Saraf

How to Identify Pore-Geophysical parameters of 2D_Thinsection_Sandstone Image by Image Processing

Thinsection_Sandstone|nullxnull

I want to measure the 2D image geophysical parameters (Porosity, Pore Diameter, Pore Throat, Connectivity between pore, Relative Permeability, Contact angle, Capillary Pressure). Is there any other macro or plugin for this ?
Image was upload above : Thinsection_Sandstone.jpeg > Scale: 150 pixels = 50 mm > Blue color showing Pore space.


8-bit grayscale image : Thinsection_Sandstone_Binary


To calculate Porosity, I am using BoneJ Plugin > Fraction > Area/Volume Fraction and Result table shows Porosity(Area Ratio).


To Calculate Pore Diameter, I am using BioVoxxel Plugin > Extended Particle Analyzer and Result can’t shows. It is showing error like this:

Error …Exception >

(Fiji Is Just) ImageJ 2.0.0-rc-69/1.52i; Java 1.8.0_172 [64-bit]; Windows 7 6.1; 97MB of 1511MB (6%)
 
java.lang.IllegalArgumentException: Row out of range
	at ij.measure.ResultsTable.getValue(ResultsTable.java:387)
	at Extended_Particle_Analyzer.particleAnalysis(Extended_Particle_Analyzer.java:475)
	at Extended_Particle_Analyzer.run(Extended_Particle_Analyzer.java:321)
	at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:266)
	at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:114)
	at ij.IJ.runUserPlugIn(IJ.java:230)
	at ij.IJ.runPlugIn(IJ.java:192)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:748) **

So I am Using Analyze Particles… Tools > size: 0-infinity, Circularity: 0-1 and Result table shows Area, Perimeter, Circularity, Aspect Ratio, Roundness, Solidity then How could i analyzed, what is the diameter of pore space in 2D_Thinsection_sandstone Image ?


To calculate Pore Throat, I am using Watershed Algorithm but could not understood its result. ** Should told me about that algorithm & How it works ?**


Right now i’m struggeling to find a way to calculate my pore diameter, pore throat, relative permeability and capillary pressure between the connected pores.
Is there a common way to do it? or Plugin available for it ?

I would really appreciate it if you can give me some answers to my questions!
Thanks a lot!

Shubham

Hello Shubh94!
And a good day to you.
I’m quite sure there is a way to do what you wish, but we could really use an example (unsegmented) image to see everything involved. If you supply one in PNG or Tiff would be great but any format can be used.
Bob

Bob,

I’m sorry to state: you are slightly off…

The OP has posted the original image already. Here is the link:
https://aws1.discourse-cdn.com/business4/uploads/imagej/original/3X/a/e/ae605c6a282cf37fd703fe6a613627dc5ea819e7.tif

Regards

Herbie

Hello folks,
It’s o.k. to let Herbs’ post to me. He’s trying to help.
Bob

Hello Bob!
Have a Good day and sorry to let reply…
Thinsection_Sandstone|nullxnull
This Image, I want to Analyze Particles with Pore-space parameter (Porosity, Relative Permeability, Capillary Pressure).


This is Segmented Image of Blue part from origin image.

I’m struggling to find a way to calculate pore diameter, pore throat, relative permeability and capillary pressure in thinsection image ?
Is there a common way to solved it? or other Plugin available for that image processing in Petroleum-Geoscience parameter defined?

Thank you for reply!
Regards

Shubham

Hello Herbie!
Have a Good day and thanks for your consideration in blog…

Thinsection_Sandstone|nullxnull
This Image, I want to Analyze Particles with Pore-space parameter (Porosity, Relative Permeability, Capillary Pressure).


This is Segmented Image of Blue part from origin image.

I’m struggling to find a way to calculate pore diameter, pore throat, relative permeability and capillary pressure in thinsection image ?

Is there a common way to defined above parameters? or other Plugin available for that image processing in Petroleum-Geoscience parameter defined?

Thank you!
Regards

Shubham

Good day Shubham!

pore diameter, pore throat

These are parameters that in principle can be extracted from images, at least their 2D extensions with respect to the plane of the thinsection.

I’m not aware of specialized code that does provide both measures.
In any case, have a look at BoneJ.

relative permeability and capillary pressure

These parameters appear only indirectly related to what can be extracted from an image of a thinsection.

I’m not acquaited with your field of research, so I can’t help with definitions etc.

Good luck

Herbie

I guess that the pore throat is the smallest diameter between pore cavities.
Apparently this reference describes some way of do it, but it is behind a pay-wall:

http://archives.datapages.com/data/bulletns/1990-91/data/pg/0075/0010/0000/1547.htm

I suspect that you would need 3D data to do that accurately, not 2D sections.

Hello once again Shubh94,
After having read both the reference article and the BoneJ documentation and what little I know about anything I am confident that what you wish to determine can be done, however it won’t be really quick for someone in a hurry so be patient and we can all work on it.

First take the second segmented image you provided and goto Edit > Invert and invert the image. Take your original Tif image (RGB) then goto Process > Image Calculator and put the original image in the top name area and the second segmented image in the bottom name area and set the operation to “Subtract”. That is the actual Blue part of the image which I understand is the first important part. Do NOT Binarize it, you need the dynamic range for further analysis but you can (and should change it) to 32bit type, save this result. You can apply a LUT to see the range you have to work with, I used the 16 color lut.

While you are doing this and playing with it I will work on planning a work flow to accomplish the other objectives you are aiming for, so I’ll get back soon.
Bob

Hello Herbie,
sorry for let reply.

ok.
I am looking BoneJ plugin and try to understand its operation of Analyze particles.

Have a Good Day !
Thanks for your consideration !

Shubham

Hello Gabriel,

In that 2D_Thinsection_Sandstone Image blue color was showing Pore space so after segmentation I can defined porosity by differentiation in black-white pixel and using BoneJ > Area/Volume Fraction and got result table.

For Pore Throat :
You are understanding right pore throat is the smallest length which connect two pore in segmented thinsection image so to identify it I am using Skeleton tool from BoneJ plugin but it shows breaks line between some connection so I am required some better image processing technique to solve it and also I am working with number of thinsections of one core sample so after merge all with different thickness parameter its convert 2D to 3D and then some experimental work done on core sample I can actually identify my Pore Network Model.

I was refer some Thesis paper link = https://oaktrust.library.tamu.edu/bitstream/handle/1969.1/164570/VALENZUELA-DOCUMENT-2017.pdf?sequence=1&isAllowed=y
It also going to help me to identify my parameter by Image Processing.

Thank you for your consideration !
Shubham

Good day to Bob,

As you explain early process that I was done but at last I got that kind of result Image
= Result%20Image|nullxnull
On that image I am applying Threshold... > Make Binary > BoneJ_Area Fraction > Result table
= Result%20Table

But using Analyze particle tool it can show only area other parameter can’t show.
and I was already done to calculate pore space from Thin section image by that image processing technique but now I’m struggling with Pore Throat - Relative permeability - contact angle Identification process.

point_up_2:Yes I’m understand each and every one have busy work schedule.

Thank you for your consideration !

Shubham

Hello Shubh94 and Happy New Year to you and yours’,
I am pleased that you used the complete image to work with. The color differences in the original image only showed which areas are more porous than others. And the BoneJ results were because it selected the entire image for analysis, but your making a good start.
What you need next is to select the areas based on size AND shape which you can do with a plug - in for “Shape Filter” which you can obtain via (in their words)“You could simply use our update site “Biomedgroup” to install the shape filter plugin.” which you will use very often in the future to determine both size, shape and many other perimeters you need to continue on.
Also you need to set measurements in Analyze to also set Shape descripters, Area fraction,Fit ellipse and Feret’s diameter for future use. And the mean background on the image you attached had a value of 4, so you should use Process > Math > Subtrack 4 to make it easier to determine areas for segmentation.
You are making a good start, and you will be able to determine all the values you need exactly as presented in the reference paper. They had to input all of the same perimeters as you need to, so their software will not work any better.
Play with the new plug-in and learn how to use it also so that it and BoneJ may be all you will need. It’s a steep learning curve but I’m sure you can handle it.
Update me frequently if you need support and such. Good luck,
Bob