Automatic Morphological Reconstruction of Neurons from Multiphoton and Confocal Microscopy Images Using 3D Tubular Models

The challenges faced in analyzing optical imaging data from neurons include a low signal-to-noise ratio of the acquired images and the multiscale nature of the tubular structures that range in size from hundreds of microns to hundreds of nanometers. In this paper, we address these challenges and present a computational framework for an automatic, three-dimensional (3D) morphological reconstruction of live nerve cells. The key aspects of this approach are: (i) detection of neuronal dendrites through learning 3D tubular models, and (ii) skeletonization by a new algorithm using a morphology-guided deformable model for extracting the dendritic centerline. To represent the neuron morphology, we introduce a novel representation, the Minimum Shape-Cost (MSC) Tree that approximates the dendrite centerline with sub-voxel accuracy and demonstrate the uniqueness of such a shape representation as well as its computational efficiency. We present extensive quantitative and qualitative results that demonstrate the accuracy and robustness of our method.