Amira is a flexible 3D software with special strength in manual segmentation and assignment of 3D structures. Data from lightsheet microscopy, CT or sectional TEM can be segmented using a large palette of tools. Surfaces can be displayed and exported as snapshots or movies. Programming in Python or Matlab is possible if users are experienced in these languages.
Selection of projects already done
3D Segmentation and Editing
Segment different organs and tissues in a 3D stack.
More information can be found here (PDF).