3D Segmentation of a Binary Image

Hi all,

I currently have a stack of 1000 or so binary .tiff files that, when stacked together, become a 3D sample. I want to determine the volume of each crack in the volume. I have some ideas on how I should go about implementing it, but I thought I would get some advice before I begin.

1) Is there a tool that does exactly what I want to do out there already? I have already done multiple hours of research, but I cannot find a tool that does exactly what I need. If it exists, please share. I have looked into imagej, MATLAB, and dragonfly tools; there may be more in these that was over my head, but I am willing to use any tool (although the beginning of my project started in MATLAB).

2) Assuming there is no tool available, my plan is to find where each white pixel is (excluding the boundaries of my images) and have a nested for loop that connects each pixel at a spceified xy coordinate in adjacent files. I plan on going in depth first, and then adding each of the individual strings that are connected to other individual strings by 8 connectivity would attach. Is this the best way to go about this, assuming someone hasn't already done it?

If you have any questions about the specifics to be able to answer my problem well, please let me know! I will be as prompt as I possibly can in answering. Attached are some sample images, so you can visualize what they look like!

https://drive.google.com/drive/folders/1e9a5Y8_NhgqZQ2D0eqfB_BMjUNjlX__L?usp=sharing

[Image Processing Newbie]

I wanted to add a new idea I have just to update on the process, still hoping someone already knows of a tool! Instead of doing the method I listed above (that I have unofficially dubbed string method), I have an alternate idea I am now pursuing. I will be finding the centroid of each crack on the 2d slice, and compare the centroids of adjacent images to check for continuity of a crack. Still stuck though, so any input would be fantastic!

Answer 1

[Image Analyst]

regionprops3()