Automated neuropil segmentation of fluorescent images for Drosophila brains

The brain atlas, which provides information about the distribution of genes, proteins, neurons, or anatomical regions in the brain, plays a crucial role in contemporary neuroscience research. To analyze the spatial distribution of those substances based on images from different brain samples, we often need to warp and register individual brain images to a standard brain template. However, the process of warping and registration often leads to spatial errors, thereby severely reducing the accuracy of the analysis. To address this issue, we develop an automated method for segmenting neuropils in the Drosophila brain using fluorescence images from the FlyCircuit database. This technique allows future brain atlas studies to be conducted accurately at the individual level without warping and aligning to a standard brain template. Our method, LYNSU (Locating by YOLO and Segmenting by U-Net), consists of two stages. In the first stage, we use the YOLOv7 model to quickly locate neuropils and rapidly extract small-scale 3D images as input for the second stage model. This stage achieves a 99.4% accuracy rate in neuropil localization. In the second stage, we employ the 3D U-Net model to segment neuropils. LYNSU can achieve high accuracy in segmentation using a small training set consisting of images from merely 16 brains. We demonstrate LYNSU on six distinct neuropils or structure, achieving a high segmentation accuracy, which was comparable to professional manual annotations with a 3D Intersection-over-Union(IoU) reaching up to 0.869. Most notably, our method takes only about 7 seconds to segment a neuropil while achieving a similar level of performance as the human annotators. The results indicate the potential of the proposed method in high-throughput connectomics construction for Drosophila brain optical imaging.