High-throughput Computer Method for 3D Neuronal Structure Reconstruction from the Image Stack of the Drosophila Brain and Its Applications

Drosophila melanogaster is a well-studied model organism, especially in the field of neurophysiology and neural circuits. The brain of the Drosophila is small but complex, and the image of a single neuron in the brain can be acquired using confocal microscopy. Analyzing the Drosophila brain is an ideal start to understanding the neural structure. The most fundamental task in studying the neural network of Drosophila is to reconstruct neuronal structures from image stacks. Although the fruit fly brain is small, it contains approximately 100 000 neurons. It is impossible to trace all the neurons manually. This study presents a high-throughput algorithm for reconstructing the neuronal structures from 3D image stacks collected by a laser scanning confocal microscope. The proposed method reconstructs the neuronal structure by applying the shortest path graph algorithm. The vertices in the graph are certain points on the 2D skeletons of the neuron in the slices. These points are close to the 3D centerlines of the neuron branches. The accuracy of the algorithm was verified using the DIADEM data set. This method has been adopted as part of the protocol of the FlyCircuit Database, and was successfully applied to process more than 16 000 neurons. This study also shows that further analysis based on the reconstruction results can be performed to gather more information on the neural network. Author Summary: It is now possible to image a single neuron in the fruit fly brain. However, manually reconstructing neuronal structures is tremendously time consuming. The proposed method avoids user interventions by first automatically identifying the end points and detecting the appropriate representative point of the soma, and then, by finding the shortest paths from the soma to the end points in an image stack. In the proposed algorithm, a tailor-made weighting function allows the resulting reconstruction to represent the neuron appropriately. Accuracy analysis and a robustness test demonstrated that the proposed method is accurate and robust to handle the noisy image data. Tract discovery is one of the most frequently mentioned potentials of reconstructed results. In addition to a method for neuronal structure reconstruction, this study presents a method for tract discovery and explores the tract-connecting olfactory neuropils using the reconstructed results. The discovered tracts are in agreement with the results of previous studies in the literature. Software for reconstructing the neuronal structures and the reconstruction results can be downloaded from the Web site http://www.flycircuit.tw. More details on acquiring the software and the reconstruction results are provided in Text S1.