AbstractThe morphology of a neuron is strongly related to its physiological properties, and thus to information processing functions. Optical microscope images are widely used for extracting the structure of neurons. Although several approaches have been proposed to trace and extract complex neuronal structures from microscopy images, available methods remain prone to errors. In this study, we present a practical scheme for processing confocal microscope images and reconstructing neuronal structures. We evaluated this scheme using image data samples and associated gold standard reconstructions from the BigNeuron Project. In these samples, dendritic arbors belonging to multiple projection branches of the same neuron overlapped in space, making it difficult to automatically and accurately trace their structural connectivity. Our proposed scheme, which combines several software tools for image masking and filtering with an existing tool for dendritic segmentation and tracing, outperformed state-of-the-art automatic methods in reconstructing such neuron structures. For evaluating our scheme, we applied it to a honeybee local interneuron, DL-Int-1, which has complex arbors and is considered to be a critical neuron for encoding the information indicated in the waggle dance of the honeybee.