My research takes advantage of the detailed 3-dimensional information that can be learned from micro-computed tomography (micro-CT). Below is a list of useful resources that I have compiled during my (ongoing) education and experimentation with visualization of of micro-CT scan data. Most of my work has been with OsiriX or (increasingly) Amira, and so these resources will focus on these software tools. This page is by no way exhaustive, but it helps me curate links and helpful information so maybe it will help others too.
Comments on OsiriX vs. Amira
OsiriX has the major advantage of being open source (and the 62 bit version upgrade is very cheap compared to the other options out there). It is fairly quick and easy to visualize your data using volume rendering in Osirix. Simple region growing and selection of regions of interest work well, but more complicated segmentation quickly becomes frustrating. It should be noted that OsiriX is only for Mac.
Amira’s strength seems to be in surface rendering and segmentation. I also find the working environment makes it much easier to track your manipulation history and save your progress, which are good from a practical and publication standpoint. For comparative and quantitative analysis, I am transitioning to using Amira over Osirix. Amira is expensive and only for PC, although I still use OsiriX for quick and more appealing volume rendering.
Amira — basic info about opening files and segmentation
OsiriX — basic notes about opening files, volume rendering, and ROIs
Segmentation and suface extraction from Brown’s XROMM resources
Extract a 3D volume from a series from WikiCommons. Less useful now that the screenshots have been taken down.
Bone segmentation instructions from Brown’s XROMM resources page
OsiriX. Mac only. Upgrade to 64-Bit version highly recommended
MicroView download from SourceForge. Useful for file manipulation and conversion (e.g., .vff –> .DCM)
MicroView Quick Reference Guide.