LOADING TIFF FILES AND GENERATING A 3D PLOT SHOWING THE PORES

How can i generate a 3D plot of a tiff file for a rcok sample (that will be converted to an array) shoing just the pores in the rock

In essence what i woiuld like to do is to

Read my stack of tiff files into an array

Get porosity values

Genearte arrays of porosity

Visualize the rock pores

[Enoch]

I am trying to genrate something like this

Answer 1

[Shubh Pareek]

Hi @Enoch

To generate a 3D plot in MATLAB of a tiff file representing a rock sample with just the pores showing, you can follow these general steps:

1. To read the stack of tiff files into an array use the function "imread" to read the stack of tiff files into a 3D array in MATLAB.

image_stack = imread('sample.tiff');% use whatever is the name of your file,it should be in same directory

2. To determine the porosity values for defining the proportion of pores in the rock sample. It can be calculated by thresholding the image stack with a suitable threshold value to extract the regions corresponding to pores.

level = graythresh(image_stack);
bw_stack = imbinarize(image_stack, level);
voxel_volume = 0.03.*0.03.*0.03; % voxel volume in cubic millimeters
porosity_stack = sum(bw_stack(:)==1) ./ size(bw_stack(:),1) ./ voxel_volume;

3.To Create a 3D visualization of the rock pores , use the isosurface function to extract the pores from the thresholded image stack and create a polygonal surface for each pore. The resulting surface can be plotted using "patch" function.

pore_surface = isosurface(bw_stack,0.5);
figure;
patch(pore_surface,'FaceColor', 'blue', 'EdgeColor', 'none');
view(3);
axis tight;
daspect([1 1 1]);
light('Position',[0 0 1],'Style','infinite');
light('Position',[0 0 -1],'Style','infinite');
lighting gouraud

In this example, I used a voxel size of 0.03 mm and a threshold of the grayscale threshold that determined by the Otsu's method for binarization of the image. You may need to adjust these parameters based on the specific application.

I hope this helps with your query .

Resources for the commands used -

Extract isosurface data from volume data - MATLAB isosurface - MathWorks India

Set lighting method - MATLAB lighting - MathWorks India

Create patches of colored polygons - MATLAB patch - MathWorks India

Global image threshold using Otsu's method - MATLAB graythresh - MathWorks India

Binarize 2-D grayscale image or 3-D volume by thresholding - MATLAB imbinarize - MathWorks India

[Enoch]

Thanks@Shubh Pareek,

I followed your approach but i noticed

Error using isosurface

V must be a 3D array.

Error in Cores (line 6)

pore_surface = isosurface(bw_stack,0.5);

[Enoch]

To Replicate along the third dimension

bw_stack = repmat(bw_image, [1 1 10]); 

I added this code...

This is my result (attached)

I think now i would like to isolate just the pores and visualize that