A workflow template to analyze subcellular structures in fluorescence 2D/3D microscopy images based on a Fiji plugin Squassh is described in Rizek et al (2014).
The workflow employs detecting, segmenting, and quantifying subcellular structures. For segmentation, it accounts for the microscope optics and for uneven image background. Further analyses include both colocalization and shape analyses. However, it does not work directly for time-lapse data. A brief summary note can be found here.