Hello Manu Francis ,

yes you can use STIR for 3D reconstruction check [1] and you will find STIR paper and open source program it will be useful in this topic.

there are a lot of 3d reconstruction algorithms working under STIR. so you have to google it "STIR 3d reconstruction"

Good luck

Mohamed Samir

references:

[1] Conference Paper STIR: Software for Tomographic Image Reconstruction Release 2