Hello,
I am working with micro-CT scans of rat brains to quantify hemispheric tissue loss following Controlled Cortical Impact using the method: % Tissue loss = (Vcontra-V ipsi)/(V contra). There are three specific steps that I am looking for recommendations on.
- Our scans are frequently off-center, which makes it hard to accurately split the brain into two hemispheres.
- What approach should I take to rotate/re-slice the volume before dividing it into the left and right hemispheres?
- Once it is aligned, is there an established way to define a cutting plane to partition the brain down the midsagittal plane?
- Standardizing anatomical boundaries. The olfactory bulbs, and cerebellum were dissected prior to scanning, but some remnants remain.
- What tools are recommended to establish anterior/posterior cutoffs so that remnant tissue is excluded uniformly across all subjects?
- How do I do this without sacrificing some of the cortical area?
- Suppressing Surface Spikes/Noise. Due to noise at the tissue boundary, intensity thresholding results in a jagged dorsal cortical surface rather than smooth contour.
- Which tool can I use to preserve the true cortex without distorting the lesion area?
Any advice helps!
Thank you