Stacking 2D tiff images with a specific voxel depth for pore network extraction

[monmon564]

Hello I have 29 slices of tiff images from XTM. Each slice or image has a thickness 1 micrometer, but the spacing between each image is 8 micrometers. How do I do it using poreSpy. Below i gave part of my code for loading tif images. im = imageio.volread('C:/Users/User/Desktop/New Codes/High Porosity.tif*')
im = (im > 0).astype(bool) pn = ps.networks.snow2(phases=im,voxel_size=1e-6, accuracy='standard', parallelization=None) with this the images stack without any spacing between them

[ma-sadeghi]

Hi,
You can zoom by 8x along the axis normal to the slices, which makes the resolution of your image 8 um across all dimensions (pass voxel_size=8e-6).

How to zoom: https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.zoom.html

[monmon564]

thank you it worked.But what order and mode should be best for a porous network extraction?

[ma-sadeghi]

Use order=0 (nearest neighbor interpolation) and mode='constant' (enforces no interpolation beyond boundaries).

[jgostick]

you could technically use a higher order interpolation to "fill in" the missing layers...probably linear (order=1). Just remember to reapply a threshold to convert the image back to a boolean.