Hello, I’m am new to ImageJ and this is my first forum post.
As part of a project I am trying to determine the porosity of a soil core and how it varies with depth. I have micro X-Ray CT images of soil cores. A re-slice of the raw image from one core is below.
Reslice of Core7 - for forum post.tif (892.3 KB)
I have applied the Otsu thresholding plug-in which provides a good differentiation between the air above the soil (black), the soil (white) and the soil pores (black) as shown in the image below.
What I am trying to achieve is a calculation of the average porosity with depth below the soil surface. The reason for this is that I am studying the impact of soil crusts (which have lower porosity) upon infiltration of water into the soil profile.
As the soil surface is uneven I think that I need to flatten the soil surface in order to be able to use the analyse-measure command to calculate the porosity. Another method could be to use the colour difference between the air above the soil and the soil surface to create a line that follows the surface and then create regions of interest based on this line at regular depths below the soil surface to provide a region of interest to enable calculation of porosity.
I have not been able to work out how to achieve either of these methods and would welcome any feedback on how to do so.
Cameron from Australia