<p>Lung cancer remains a major global health challenge, and accurate pathological examination is crucial for early detection. This study aims to enhance hyperspectral pathological image analysis by refining annotations at the cell level and creating a high-quality hyperspectral dataset of lung tumors. We address the challenge of coarse manual annotations in hyperspectral lung cancer datasets, which limit the effectiveness of deep learning models requiring precise labels for training. We propose a semi-automated annotation refinement method that leverages hyperspectral data to enhance pathological diagnosis. Specifically, we employ K-means unsupervised clustering combined with human-guided selection to refine coarse annotations into cell-level masks based on spectral features. Our method is validated using a hyperspectral lung squamous cell carcinoma dataset containing 65 image samples. Experimental results demonstrate that our approach improves pixel-level segmentation accuracy from 77.33% to 92.52% with a lower level of prediction noise. The time required to accurately label each pathological slide is significantly reduced. While pixel-level labeling methods for an entire slide can take over 30 mins, our semi-automated method requires only about 5 mins. To enhance visualization for pathologists, we apply a conservative post-processing strategy for instance segmentation. These results highlight the effectiveness of our method in addressing annotation challenges and improving the accuracy of hyperspectral pathological analysis.</p>