PIGMENT: A deep learning framework for Porcine Immunohistochemistry seGMENTation

Traumatic brain injury produces widespread axonal damage can be assessed histologically using amyloid precursor protein (APP) immunohistochemistry, which labels injured axonal profiles at cellular resolution [1, 2]. However, quantification of APP pathology remains a major bottleneck: annotation is manual, time-consuming, spatially localized, and variable across raters, limiting scalability and reproducibility. This limitation is particularly important in studies that use histology as a reference for neuroimaging or other tissue-level measurements, where cellular APP pathology must be quantified in a spatial form that can be aligned with imaging abnormalities. Here, we introduce PIGMENT, an annotation-efficient deep-learning framework for automated segmentation and quantification of APP-positive pathology in porcine white matter histology. PIGMENT uses a compact SegFormer-B0 architecture trained on 525 expert-annotated 512 x 512-pixel tiles from four APP-stained sections across three pigs. Because APP-positive profiles are sparse, fragmented, stain-variable, and morphologically diverse, PIGMENT combines limited expert labels with APP-specific augmentation designed to model variation in APP-positive intensity, size, continuity, fragmentation, and local tissue context. We evaluated PIGMENT using an instance-level detection rate that measures whether discrete APP-positive components are localized. Across held-out APP-stained data, PIGMENT achieved a mean instance-level detection rate of 0.86. Across the configurations tested, the highest mean detection rate was achieved by a training set that included sections from different animals, suggesting that annotation diversity may be an important factor under limited-label conditions. By extending limited high-confidence expert annotations into whole-section APP burden maps, PIGMENT provides a scalable framework for characterizing the extent and spatial distribution of traumatic axonal injury. These maps may support future studies that align histological injury burden with imaging-derived measures.