I am a new user of 3D Slicer and am trying to measure bone density of fish across species, I am wondering if any one has any suggestion of resources that I could look into as a starting point to learn about how to do the measurement and using the software in general?
You should have everything you would need to calculate bone density in Slicer. However, be warned that proper bone density calculation requires scans in which intensity values are calibrated using known phantoms.
If your scan and image reconstruction protocol are identical across your samples, you might be able to calculate relative bone density (aka bone volume fraction), which is basically the ratio number of voxels designated as bone (e.g., after thresholding) to the total number of voxels in the region. The higher the number, the denser the bone is (ratio of 1 indicating no porosity).
The rest is having a protocol that allows you to define your regions/volume of interest consistently across your samples. This might be harder than you think in multi-species samples.