Chinmayee Athalye | Searcharxiv

arXiv2026

Automated Optical Density Normalization for Myelin Quantification: Cross-Modal Validation with 7T Ex Vivo MRI

White matter hyperintensities (WMH) are bright regions on T2-weighted magnetic resonance imaging (MRI) scans and are associated with cerebrovascular pathology and neurodegeneration, including myelin loss. While Luxol Fast Blue histopathology provides visualization of myelin integrity, quantitative analysis requires measuring Optical Density as a proxy for myelin concentration. However, differences in laboratory protocols and tissue processing introduce staining variability that acts as systematic noise, obscuring the biological signal and preventing consistent comparison across histology runs. To address this, we developed an automated pipeline that identifies reference (non-pathologic) regions in whole-slide images to compute normalized Optical Density heatmaps. We validated this approach through two complementary evaluations: (1) comparison against expert ratings of myelin loss severity, and (2) cross-modal spatial comparison with co-registered 7T ex vivo MRI for voxel-wise evaluation within white matter regions. The pipeline's reference selection showed strong concordance with expert-identified reference regions, and normalized Optical Density demonstrated a substantially stronger correlation with MRI signal intensity than raw measurements. This correlation persisted within WMH, confirming that the pipeline captures continuous myelin pathology rather than merely the presence or absence of myelin loss contrast. By mitigating staining artifacts, this pipeline provides a robust, validated framework for quantitative cross-modal comparison, establishing a critical methodological foundation for future translation to in vivo myelin mapping and biomarker discovery.

physics.med-ph↗

arXiv2022

Domain-guided data augmentation for deep learning on medical imaging

While domain-specific data augmentation can be useful in training neural networks for medical imaging tasks, such techniques have not been widely used to date. Here, we test whether domain-specific data augmentation is useful for medical imaging using a well-benchmarked task: view classification on fetal ultrasound FETAL-125 and OB-125 datasets. We found that using a context-preserving cut-paste strategy, we could create valid training data as measured by performance of the resulting trained model on the benchmark test dataset. When used in an online fashion, models trained on this data performed similarly to those trained using traditional data augmentation (FETAL-125 F-score 85.33+/-0.24 vs 86.89+/-0.60, p-value 0.0139; OB-125 F-score 74.60+/-0.11 vs 72.43+/-0.62, p-value 0.0039). Furthermore, the ability to perform augmentations during training time, as well as the ability to apply chosen augmentations equally across data classes, are important considerations in designing a bespoke data augmentation. Finally, we provide open-source code to facilitate running bespoke data augmentations in an online fashion. Taken together, this work expands the ability to design and apply domain-guided data augmentations for medical imaging tasks.

cs.CV↗