I am attempting to segment out my entire animal specimen. I am starting with the threshold tool but it is including too much background noise. The inside of the specimen has many little circles and bubbles. Is there an easy way for me to get rid of these small circles/air pockets? Besides going over it with the paint tool.
Those can be effectively cleaned using different effects such as islands, scissors and or margin tools. I would encourage you to get yourself familiar with segmentation process in Slicer.
This is where you can start
https://github.com/SlicerMorph/Tutorials/blob/main/Segmentation/README.md