Hi,

Image J can do almost you want. Volume J for 3D reconstruction from 2D stack. There are also plugins to analyze mitochondrial morphology, but you can do it manually from skeletonized image of your mitos, for example, or easyly analyzing size, number, perimeter, lenght of your objects (mitos). 

http://imagejdocu.tudor.lu

Good luck

Hi,

Image J can do almost you want. Volume J for 3D reconstruction from 2D stack. There are also plugins to analyze mitochondrial morphology, but you can do it manually from skeletonized image of your mitos, for example, or easyly analyzing size, number, perimeter, lenght of your objects (mitos). 

http://imagejdocu.tudor.lu

Good luck

In addition to the above, you might then want to analyze the link structure of the vertices of the 3D skeleton, i.e., the average number of links per vertex.

Thank you both for the suggestions - I will look into the Image J plugin for mitochondrial morphology analysis and link structure analysis!