LLM-enhanced Neuron Segmentation and Reconstruction in Complex Mouse Brain Images

Neuron segmentation in complex mouse brain images improves neuron reconstruction and supports studies of brain structure and function, while the existing deep learning-based methods do not sufficiently exploit prior information, including neuronal morphology and imaging mechanism. We propose NUNet-LLM, the first LLM-integrated framework for neuron segmentation and reconstruction. NUNet-LLM consists of an LLM-based text path and a 3D UNet-based image path to extract and fuse multi-modal features, guiding the deep model to better focus on slender nerve fibers. The text path leverages two pre-trained LLMs to generate dataset- and task-level textual descriptions and compute static textual features in advance, so no additional LLM inference is required during testing. The image path combines a 3D UNet with wavelet transform and an attention mechanism; its encoder extracts robust image features, and after fusion with textual features, its decoder predicts segmentation masks. To train NUNet-LLM, we constructed a mouse brain neuronal cube dataset (mNeuCuDa) from 18 manually annotated neurons in mouse brain images, and introduce a synthetic dataset (sNeuCuDa) to reduce interference from the unlabeled nerve fibers. In addition, we designed a topology structure loss by combining cross-entropy, structure loss, and edgeaware loss. After segmenting, an automatic algorithm was applied to reconstruct intertwined neurons in the neuronal images, and G-Cut was utilized to decouple them. Experiments on mouse brain neuronal images and BigNeuron demonstrate the effectiveness of NUNet-LLM for neuron segmentation and reconstruction.