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

Abstract

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.

Learning Context Cues for Synapse Segmentation

“…For example, evidence obtained from EM images suggests that the size, shape and distribution of synapses vary during the course of normal life but also under specific pathological conditions [27]. Similarly, EM imaging has provided new insights into synaptic signaling [21] and its relationship to mitochondrial activity [25] as well as to some neuro-degenerative diseases [19], [32].…”

Neuronal Morphology Goes Digital: A Research Hub for Cellular and System Neuroscience

“…Chiang et al, 2011; Peng et al, 2011). In particular, the software that enabled the first (and so far only) high-throughput reconstruction study, 16,000 drosophila neurons (Lee et al, 2012), can be downloaded as executable for different operating systems (flycircuit.tw/NT/Win32.zip; flycircuit.tw/NT/Win64.zip; flycircuit.tw/NT/Linux_x86.zip), but lacks user-friendly documentation.…”

Doubling up on the Fly: NeuroMorpho.Org Meets Big Data

“…The 2010 DIADEM competition (DiademChallenge.org) helped foster considerable advances towards tracing automation 5 and was followed one year later by the large-scale reconstruction of more than 16,000 Drosophila neurons 6 . The public posting of all image stacks and corresponding digital tracings on flycircuit.tw after an additional year 7 constituted the first (and so far only) success in high-throughput digital morphology.…”