A General Deep Learning framework for Neuron Instance Segmentation based on Efficient UNet and Morphological Post-processing
This work addresses the labor-intensive annotation problem in medical image analysis for preclinical studies of neurodegenerative diseases, offering an incremental improvement over existing methods.
The paper tackles neuron instance segmentation in histological images by proposing a framework that uses point annotations to synthesize pixel-level masks for training an EfficientNet-UNet model, achieving superior performance compared to recent methods. It also introduces a novel post-processing strategy based on ultimate erosion and dynamic reconstruction that outperforms classical techniques.
Recent studies have demonstrated the superiority of deep learning in medical image analysis, especially in cell instance segmentation, a fundamental step for many biological studies. However, the excellent performance of the neural networks requires training on large, unbiased dataset and annotations, which is labor-intensive and expertise-demanding. This paper presents an end-to-end framework to automatically detect and segment NeuN stained neuronal cells on histological images using only point annotations. Unlike traditional nuclei segmentation with point annotation, we propose using point annotation and binary segmentation to synthesize pixel-level annotations. The synthetic masks are used as the ground truth to train the neural network, a U-Net-like architecture with a state-of-the-art network, EfficientNet, as the encoder. Validation results show the superiority of our model compared to other recent methods. In addition, we investigated multiple post-processing schemes and proposed an original strategy to convert the probability map into segmented instances using ultimate erosion and dynamic reconstruction. This approach is easy to configure and outperforms other classical post-processing techniques. This work aims to develop a robust and efficient framework for analyzing neurons using optical microscopic data, which can be used in preclinical biological studies and, more specifically, in the context of neurodegenerative diseases.