I wanted to know your opinion on which measurement from 3DOC to use for characterizing 3D structures inside the cell in images taken with a confocal microscope: Surface or Volume? Are both equally affected by lower z resolution?
It would be hard to suggest or opinion about the measurement without knowing the context. Generally any measurement with confocal image with lower Z-resolution have to be considered with caution. Of course it depends on the context and what your are trying to measure. For example, if you are trying to measure a small vesicle structure like an autophagosomes, you need to have a very good Z-resolution. I think we can help you better if you could provide more details regarding your problem with some sample images if possible.