• 3D viewing during segmentation
• Cutting away unwanted parts in 3D
• Digital dissecting
• Extracting separate surfaces
• From 3D landmarks to MorphoJ file
• Generate new stack of slices from a different orientation
• Miscellaneous Amira tools
• Using a stack file for histological section images
• Using histological sections for reconstructing in Amira (short manual, old version of Amira)
• Visualising colored orthoslices