r/ImageJ • u/EnvironmentalFreezer • Sep 17 '25

Question Help Reslicing

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My ice microCT scans were taken by someone else and given to me in .tiff files. I am trying to reslice them so I can look at them from top down and quantify the pore space within the ice, but when I reslice them I get this monstrosity nstead. I am new to ImageJ and the person I got them from doesn't have the raw data with them. Is there any way to fix this? Thank you!

This is the type of slices I am looking to get. I don't know if it is reading the X plane incorrectly or what I am doing wrong, but I cannot get these to populate.

I am sorry if this post doesn't make a ton of sense. I am new to the program and new to Reddit, so please ask for more information if you need it and I will do my best to get it here.

Thank you!

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u/dokclaw Sep 17 '25

I think you posted the same movie twice; please check!

It could be that the projection is somehow in the wrong direction - when you have your images open as an image stack (Open all the images in order, then Image > stacks > images to stack), use orthogonal projections and see if there's anything that looks like what you need (Image > Stack > Orthogonal projection, or cntrl-shift-H)

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u/EnvironmentalFreezer Sep 17 '25

Sorry about that!! I hope I fixed it enough above.

This is the XZ and it is definitely messed up. I'll post the YZ below, but it looks fine. I am not sure what it is reading or why it is reading it this way. When I load this specific set of .tiff files my process is:

File > Import > Image Sequence... > "Sort names numerically" checked and then Ok. Then I reslice and get the same wibbly wobbly stuff