I’ve just started toggling around with ImageJ in the last few weeks so I apologize in advance for the generality of this question.
I’m looking to describe sheep knee morphology, focusing separately on the distal femur, patella and proximal tibia. I have CT images of these structures, but I need to segment the patella away from the femur in order to analyze the articulating surfaces. I’ve tried cutting the patella away, in every single image in the stack, but I end up compressing the stack along the z-axis when doing so. I think this has to do with altering the pixels in the specific images within the stack? I’ve been playing around with weka segmentation too, assigning different classes to the three bones and surrounding soft tissue, but I’m not sure how I would even go about extracting these segments from there.
My end goal is to create 3D surface plots of the femur, patella and tibia separately. I can do this from the original stack of DICOM files, but haven’t been able to do so yet successfully with the altered images.
I’m looking for broad strokes of advice here, plugins to use, etc. Thank you all for your time and I appreciate any advice that you can throw my way!