Automated segmentation of neurons and spinal cord structures in immunofluorescence images using SpineDL

In this study, we present SpineDL, an open-source deep learning (DL) approach for neuron and anatomical structure segmentation of the spinal cord in fluorescence images immunostained with NeuN and DAPI, within the context of murine models of spinal cord injury (SCI). SpineDL comprises two main modules: SpineDL-Neuron, for instance-level identification of neuronal somas; and SpineDL-Structure, for semantic segmentation of key spinal cord structures including gray matter, white matter, ependyma, and damaged tissue. To train the models, we developed the SpineDL dataset, a curated collection of 161 confocal images of mouse spinal cord, manually annotated by SCI researchers and organized into specific subsets. Both models are based on the HRNetV2-W64 architecture and were trained using state-of-the-art data augmentation and optimization techniques, implemented within the BiaPy framework, following an iterative refinement process driven by quantitative evaluation, SCI researcher feedback, and systematic error analysis. Our results demonstrate that SpineDL achieves researcher-level performance in both structural segmentation and neuron identification tasks, showing high robustness across anatomical regions and injury conditions. Overall, this work provides a reproducible and extensible platform for quantitative analysis of neuron distribution in the naïve and injured spinal cord, supporting automation, standardization, and scalability of histopathological workflows in neuroscience research and preclinical studies and translational applications.