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Biomedical Optics Express

Optica Publishing Group

Preprints posted in the last 7 days, ranked by how well they match Biomedical Optics Express's content profile, based on 84 papers previously published here. The average preprint has a 0.06% match score for this journal, so anything above that is already an above-average fit.

1
Assessing Lipid Core Burden Index with Depolarization-Sensitive Optical Frequency Domain Imaging

Jones, G.; Otsuka, K.; Fujisawa, N.; Yamaura, H.; Matsumoto, K.; Okamoto, A.; Yamaguchi, T.; Shimada, T.; Kagawa, S.; Yamazaki, T.; Akasaka, T.; Bouma, B. E.; Villiger, M.; Fukuda, D.

2026-06-01 cardiovascular medicine 10.64898/2026.05.22.26353889 medRxiv
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Background: Quantitative lipid assessment is central to identifying rupture-prone coronary plaques and represents a therapeutic target for lipid-lowering therapy. Near-infrared spectroscopy (NIRS)-derived lipid core burden index (LCBI) is well validated and widely used for detecting lipid-rich lesions. Optical frequency domain imaging (OFDI) is increasingly adopted for guiding percutaneous coronary intervention (PCI) due to its high-resolution structural imaging capabilities. Depolarization-sensitive OFDI (depOFDI) provides intrinsic lipid contrast and may enable combined structural and compositional plaque characterization within a single OFDI-based platform. Objective: To define an OFDI-derived lipid metric and evaluate its agreement with NIRS-derived LCBI. Methods: Thirty-three patients underwent both polarization-sensitive OFDI and NIRS-intravascular ultrasound imaging during PCI. After exclusion of 4 datasets, 29 co-registered pullbacks were analyzed. A signal-to-noise-corrected depolarization metric was used to identify lipid-rich regions and generate depOFDI chemograms. maxLCBI4mm value and location, as well as total LCBI, were computed and compared with NIRS. Results: depOFDI demonstrated strong agreement with NIRS, showing high correlation for maxLCBI4mm (r^2 = 0.862) and total LCBI (r^2 = 0.867), along with strong spatial concordance for the location of the maxLCBI4mm (r^2 = 0.900). Bland-Altman analysis of LCBI4mm showed minimal bias (10.7) with 95% limits of agreement of [81.4 to 102.8]. Conclusions: depOFDI enables accurate quantification of lipid burden alongside the high-resolution structural information inherently provided by OFDI. Because depolarization metrics can be derived from polarization-diverse detection available in many commercial OFDI systems, this approach provides a practical pathway toward comprehensive plaque characterization within existing PCI workflows, without the need for additional imaging modalities.

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High Resolution Multi-depth Quantification of the Retinal Nerve Fiber Layer

Callet, C.; Bertrand, M.; Guzman, K.; Mece, P.; Rossi, E. A.; Grieve, K.

2026-06-01 ophthalmology 10.64898/2026.05.22.26353127 medRxiv
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The retinal nerve fiber layer, composed of axon bundles converging toward the optic nerve, is a key biomarker for diagnosing and monitoring glaucoma and other neurodegenerative diseases. High-resolution en face imaging of individual nerve fiber bundles offers morphological information beyond what conventional optical coherence tomography provides, yet clinical integration remains limited by the lack of automated analysis tools and normative data. Here, we imaged 14 healthy volunteers using time-domain full-field optical coherence tomography and adaptive optics scanning laser ophthalmoscopy, and developed automated pipelines to quantify bundle width, trajectory, tortuosity, and orientation. Bundles were on average 25% wider at shallower retinal depths, width measurements were consistent across imaging modalities, and estimated axon count per bundle decreased significantly with age. Global trajectory analysis revealed systematic deviations of high resolution data from existing mathematical models, particularly in the temporal sector, leading us to propose two refined trajectory models. These normative results provide a foundation for high resolution biomarkers for use in investigations of retinal neurodegeneration.

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VOGeo-Gaze: Calibration-Free, Geometry-Aware Deep Learning for Real-Time Gaze Tracking in Clinical Video-Oculography

Zhao, J.; Ahmadi, S.-A.; Decker, J.; Zwergal, A.; Eulenburg, P. z.; Flanagin, V. L.; Wuehr, M.

2026-05-29 health informatics 10.64898/2026.05.27.26354254 medRxiv
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Quantitative eye movement analysis is important for neuro- logical diagnostics, yet existing video-oculography (VOG) systems typ- ically require calibration, device-specific settings, or accurate gaze la- bels. We present VOGeo-Gaze, a real-time, calibration-free, geometry- aware neural network that estimates gaze by reconstructing anatomi- cally meaningful eyeball parameters from image features. The method combines segmentation-driven projection geometry, a refraction-aware pupil correction module, and temporal anatomical stabilization, so gaze is derived from interpretable eye geometry rather than direct angular regression. Trained only on the public TEyeD dataset with weak gaze supervision, VOGeo-Gaze was evaluated on 116 clinical recordings from 17 patients and 19 healthy subjects using EyeSeeCam, a clinical gold- standard VOG system. It achieved median absolute angular errors of 0.33{whitebullet} horizontally and 0.35{whitebullet} vertically, with nearly 92% of recordings below 1{whitebullet} error while operating at >300 FPS. These results demonstrate sub-degree clinical gaze estimation without subject-specific calibration, camera intrinsics, or accurate gaze labels, providing a scalable and inter- pretable alternative to conventional VOG pipelines. Code is available at https://github.com/DSGZ-MotionLab/VOGeo-Gaze.

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Comparative Study on Image Quality of Deep Learning and Adaptive Statistical Iterative Reconstruction-V in Thin Layer CT of liver Lesions

Yang, J.; Li, L.; Cao, J.; Zhang, J.

2026-05-26 radiology and imaging 10.64898/2026.05.23.26353923 medRxiv
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Objective:This study aims to compare the advantages and disadvantages of DLIR and adaptive statistical iterative reconstruction-V (ASIR-V) in thin-slice (2.5 mm) CT images of hepatic lesions characterized by high and low contrast. Additionally, the study seeks to determine the optimal DLIR strength for the evaluation of liver lesions. Methods:A retrospective analysis was performed on 90 patients who underwent abdominal contrast-enhanced CT scans. Group A comprised 48 patients with low-contrast lesions, while Group B included 42 patients with high-contrast lesions. The acquired images were reconstructed using post-processing DLIR at low (DLIR-L), medium (DLIR-M), and high (DLIR-H) strengths, all with a slice thickness of 2.5 mm (subgroups A1-A3, B1-B3). Furthermore, images were reconstructed with ASIR-V at 50% strength at slice thicknesses of 2.5 mm and 5 mm (subgroups A4/B4 and A5/B5, respectively). CT values and standard deviations (SD) of the liver and lesions were measured, and the corresponding signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) were calculated. The edge rise slope (ERS) was determined using ImageJ software by measuring CT values along a line from the liver parenchyma to the lesion. Objective metrics were compared using one-way ANOVA, with independent samples t-tests applied for inter-group differences. Subjective scoring, which encompassed noise level, diagnostic confidence, and lesion margin delineation, was conducted by two radiologists, with differences analyzed using the Kappa test. Results: Objective evaluation revealed a progressive decrease in lesion SD and a progressive increase in SNR and CNR from subgroups A1/B1 to A3/B3. The SD of Group A2 decreased by 57.4% compared to A4, while the SNR and CNR of A2 icreased by 19.3% and 24.6% compared to A4. Although subgroup B2 had a lower SNR than B5, the difference was not statistically significant. SNR and CNR in B2 increased by 24.1% and 11.9%, respectively, compared to B4. ERS gradually decreased from A1/B1 to A3/B3. ERS values in A2 and B2 increased by 27.0% and 39.4%, respectively, relative to A5 and B5. Although A3 had a lower ERS than A1 and A2, all DLIR subgroups exhibited higher ERS than A5; similar trends were observed in Group B. Subjective evaluation indicated good inter-reader agreement (Kappa > 0.61, p < 0.05). As DLIR strength increased, noise scores rose progressively in both groups. However, noise in A2 and B2 was lower than in A4/A5 and B4/B5. Diagnostic confidence and lesion margin delineation scores were highest in A2 and B2, while all subjective scores were lowest in A5 and B5. Discussion: Most prior studies evaluated the liver, vessels, or confirmed that image quality can be guaranteed at low doses. However, there are few studies on specific individual lesions. Therefore, this study aims to investigate specific individual lesions. The details and detection rate were analyzed separately to confirm the clinical acceptability of 2.5-mm DLIR image in different contrast lesions. Conclusion: For both high- and low-contrast hepatic lesions, DLIR provides superior image quality compared to ASIR-V, with the 2.5mm DLIR-M setting being optimal. DLIR-M reduces image noise, improves spatial resolution, and produces images more suitable for diagnostic purposes.

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DISCERN: A Clinical Impact-aware Framework for Radiology Report Comparison

Sharma, R.; Beeche, C.; Dong, J.; Zhuang, R.; Qu, H.; Zhang, R.; Gangaram, V.; Goswami, P.; Xin, J.; Ballard, J.; Goldberg, A.; Sagreiya, H.; Long, Q.; Chen, T.; Witschey, W. R.

2026-05-27 radiology and imaging 10.64898/2026.05.26.26353612 medRxiv
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The surge in medical imaging has spurred the development of vision-language models (VLMs) to alleviate radiologist workloads. However, clinical deployment is hindered by the lack of meaningful evaluation frameworks. Current metrics - ranging from semantic similarity to large language model (LLM) based judges - often fail to distinguish between clinically trivial and critical discrepancies, poorly reflecting real-world clinical judgment. To address this, we introduce DISCERN (Discordance and Significance-aware Entity-level Radiology Report Comparison). DISCERN is a significance-aware framework that weighs report errors based on their potential impact on patient care. Our results demonstrate that DISCERN powered by closed source LLMs aligns more closely with expert radiologist assessments than traditional metrics or current LLM evaluators, providing a more interpretable and clinically relevant benchmark. By modeling radiologist prioritization and entity-level feedback, DISCERN facilitates targeted model refinement and ensures the safer integration of generative AI into clinical workflows.

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Voxel-wise temporal decomposition of hypoxia-targeted BOLD MRI: method development and proof-of-concept application in glioblastoma

Schmidlechner, T.; Stumpo, V.; Jehli, E.; Zerweck, L.; Bellomo, J.; Gönel, M.; Müller, F.; Sebök, M.; Bink, A.; Kulcsar, Z.; Weller, M.; Regli, L.; Fierstra, J.; van Niftrik, C. H. B.

2026-05-29 radiology and imaging 10.64898/2026.05.27.26354265 medRxiv
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Hypoxia-targeted BOLD MRI is a novel technique, which probes oxygenation physiology in response to a controlled transient hypoxia stimulus. In glioblastoma, the signal response is spatially and temporally heterogeneous. We developed a voxel-wise temporal decomposition framework for hypoxia-targeted BOLD MRI that separates the arrival of responses, transition phases, and steady state during controlled isocapnic hypoxia. Twenty healthy controls underwent 3-T BOLD MRI during a double hypoxic step challenge to establish a normative reference. Three patients with newly diagnosed glioblastoma were included as proof-of-concept cases. For each voxel, we estimated response arrival delay (Delaycorr), delay to plateau, delay to return and an O2-normalized steady-state response (HypoxiaSS). Healthy-control maps were used to construct a voxel-wise normative atlas and, for HypoxiaSS, a global-response-adjusted model for patient deviation mapping. In healthy controls, HypoxiaSS showed lower supratentorial between-subject variabilitythan both whole-stimulus comparators (coefficient of variation: 1.77 versus 2.36 for Hypoxiaavg) and higher voxel-level step-to-step agreement (ICC(2,1): median 0.951 versus 0.792 for Hypoxiaavg). Whole-stimulus averaging exhibited a systematic step-2 signal amplification present in 19 of 20 subjects, which was absent from HypoxiaSS. Asingle global response scalar explained a median 72.5% of voxel-wise between-subject variance in HypoxiaSS. In proof-of-concept patient analyses, G-adjusted HypoxiaSS deviation maps and timing maps identified spatially coherentabnormalities that were partly complementary and extended beyond conventional MRI-defined lesion margins.Temporal decomposition improves the stability and interpretability of hypoxia-targeted BOLD MRI and provides a practical framework for population-referenced physiological mapping and atlas-based deviation mapping in glioblastoma.

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From CCTA to Surgical Strategy: An Integrated AI Framework for Patient-Specific Coronary artery bypass grafting Planning

Rezaeitaleshmahalleh, M.; Masoumi, S.; Debalme, E.; Sundt, T. M.; Aranki, S. F.; Shin, B.; Nezami, F. R.

2026-06-01 cardiovascular medicine 10.64898/2026.05.28.26354400 medRxiv
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Background: Coronary artery bypass grafting (CABG) remains the standard of care for complex multivessel and left main coronary artery disease. However, current preoperative planning remains largely subjective, relying on qualitative interpretation of coronary CT angiography (CCTA), operator-dependent stenosis grading, and fragmented multi-software workflows. Invasive fractional flow reserve (FFR), the reference standard for physiologic lesion assessment, is infrequently acquired preoperatively, leaving distal anastomosis planning without an objective hemodynamic basis. Methods: We developed a fully automated, AI-powered platform that converts routine CCTA into a patient-specific CABG planning workflow through five integrated modules: nnU-Net based segmentation of coronary lumen and calcification; quantitative morphological and topological characterization generating more than thirty descriptors; automated stenosis detection using a local reference-radius formulation; a nine-point composite scoring framework for distal anastomosis site selection incorporating luminal caliber, landing-zone length, calcification burden, distal perfusion reserve, and bifurcation proximity; and interactive virtual graft construction coupled to a distributed reduced-order solver for pre- and post-bypass FFR estimation. Results: Lumen segmentation achieved a mean Dice similarity coefficient of 0.96 {+/-} 0.01, whereas calcium segmentation achieved 0.73 {+/-} 0.15 on the held-out cohort. Platform-derived FFR demonstrated strong agreement with invasively measured FFR (r=0.96, mean absolute relative difference 1.73 {+/-}1.42%) across the evaluated lesions, supporting the physiologic validity of the reduced-order hemodynamic solver. End-to-end analysis from raw CCTA to hemodynamic assessment and virtual graft planning was completed in approximately seven minutes per case on a standard workstation, representing a substantial reduction in processing time compared with conventional multi-tool and CFD-based workflows. Conclusions: The proposed platform demonstrates the feasibility of rapid, reproducible, and physiology-informed CABG planning using routine CCTA. By integrating anatomical characterization, automated target-site analysis, virtual graft construction, and reduced-order hemodynamic assessment into a single workflow, the framework provides objective, quantitative surgical decision support compatible with routine clinical workflows. Keywords: Coronary artery bypass grafting (CABG); Fractional flow reserve (FFR); Coronary CT angiography (CCTA); Surgical planning

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Automated Segmentation of Cerebral Arteries on Three-Dimensional Rotational Angiography Using nnUNet v2: Prospective Validation with Quantitative Metrics and Expert Qualitative Assessment

Hofmeister, J.; Brina, O.; Rosi, A.; Bernava, G.; Reymond, P.; Muster, M.; Lovblad, K.-O.; Machi, P.

2026-05-26 radiology and imaging 10.64898/2026.05.20.26353640 medRxiv
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Background: Three-dimensional visualization and quantitative analysis of cerebral arteries on 3DRA are central to endovascular treatment planning, device selection, and cerebrovascular research. Manual segmentation is time-consuming and operator-dependent, yet no open-source deep learning model has been prospectively validated for this task on 3DRA. Methods: A nnUNet v2 model was trained for binary cerebral artery segmentation on 400 consecutive 3DRA acquisitions from three angiographic systems, comparing four configurations across architectures and loss functions. The best-performing configurations were prospectively validated on 40 patients using a dual approach: quantitative metrics (DSC, clDice, HD95, ASD, Precision, Recall), and blinded expert qualitative evaluation by two interventional neuroradiologists assessing 12 arterial segments, a global quality score, and clinical usability across 40 test cases. Results: The ensemble model achieved median DSC 0.917, clDice 0.932, and HD95 1.494 mm. Global quality scores were significantly lower for nnUNet v2 than for expert segmentations (median 4 vs 5, p<0.001), but nnUNet v2 segmentations were rated clinically usable in 88-90% of cases versus 95-98% for expert segmentations, without significant difference on the binary usability criterion. A consistent proximal-to-distal quality gradient was identified, with comparable scores at proximal arteries and the largest differences at distal arterial segments. Conclusion: nnUNet v2 with topology-aware training provides clinically usable cerebral artery segmentations on 3DRA, prospectively validated through both quantitative metrics and structured expert qualitative assessment, and represents a reproducible open-source foundation for endovascular and research applications.

9
Intravital mid-infrared biosensing by normalized spatial probing of self-referenced optothermal signals

Berger, C. G.; Puttfarcken, B.; Qiu, J.; Hauer, I.; Herr, S.; Juestel, D.; Pleitez, M. A.

2026-05-28 endocrinology 10.64898/2026.05.27.26354202 medRxiv
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We present a compact pump-and-probe mid-infrared Optothermal Spectrometer (OTHES) equipped with Spatial Probing and Autocorrection (SPAC) optimized for robust intravital application in humans. SPAC-OTHES facilitates alignment stability and spectral comparability across different measurement sessions involving different skin types. Contrary to state-of-the-art, SPAC-OTHES uses camera-based beam detection and an auto-calibration mechanism that enables ca. 73% better spectral reproducibility in intravital measurements in human volunteers than non-calibrated readouts. Moreover, SPAC-OTHES has the potential to lower the glucose quantification error, as demonstrated here in artificial skin phantoms, where an improvement of 52% compared to conventional diode-based detection was observed. The compactness of OTHES, combined with reliable SPAC-readout, has the potential to accelerate commercialization and broad application of biosensors based on mid-infrared spectroscopy.

10
Deriving OCT-Equivalent Retinal Nerve Fiber Layer Thickness Maps from Fundus Photographs with Deep Learning Improves Glaucoma Diagnosis

Shi, L.; Shi, M.; Chung, I. Y.; Pasquale, L. R.; Shen, L. Q.; Wang, M.

2026-05-27 ophthalmology 10.64898/2026.05.26.26354047 medRxiv
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Purpose: To develop and evaluate a deep learning model that predicts optical coherence tomography (OCT)-equivalent retinal nerve fiber layer thickness (RNFLT) maps directly from color fundus photographs and to assess their diagnostic value for glaucoma detection. Design: Retrospective model development and evaluation study. Participants: 15,031 paired fundus photographs and spectral-domain OCT scans collected at Massachusetts Eye and Ear between 2011 and 2022. Methods: Paired fundus and OCT images were used to train a U-Net-based model to predict pixel-wise RNFLT maps with artifact-corrected supervision. Diagnostic performance was evaluated across single-modality models (fundus photos only, real RNFLT maps, predicted RNFLT maps) and multimodal fusion models (fundus + predicted RNFLT maps). Stratified analyses examined model performance across glaucoma severity and demographic subgroups. Glaucoma was defined based on standard criteria applied to Humphrey 24-2 visual field testing. Main Outcome Measures: Mean absolute error (MAE) and structural similarity index (SSIM) for RNFLT map prediction. Area under the ROC curve (AUC) and accuracy for glaucoma detection. Results: RNFLT map prediction achieved a MAE = 15.4 m and a SSIM = 0.65, measured against artifact-corrected RNFLT maps derived from OCT. For glaucoma detection, the predicted RNFLT-only classifier outperformed the fundus-only classifier (AUC 0.889 vs 0.883, p < 0.005; Accuracy 82.0% vs 78.0%), but performed worse than the real-RNFLT-only classifier (AUC 0.889 vs 0.903, p < 0.005). Multimodal fusion of fundus images with predicted RNFLT maps improved performance, achieving an AUC of 0.909, outperforming all single-modality inputs (p < 0.005 vs fundus-only, predicted-RNFLT-only, and real-RNFLT-only). Performance gains between the fundus-only and the multimodal classifier were greater in early-stage glaucoma compared to severe cases: accuracy increased from 55.3% to 64.0% in mild cases, from 71.5% to 80.4% in moderate cases, and from 90.0% to 94.6% in severe cases. Conclusions: Predicted RNFLT maps derived from fundus photographs provide quantitative, OCT-like structural information and improve glaucoma detection. Unlike prior work that predicted only summary RNFLT values, our model generates full RNFLT maps that better support glaucoma classification than fundus images alone. This approach offers a scalable pathway for early glaucoma screening and expands diagnostic access in resource-limited settings.

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Weight-Guided Constraints for Body Model and Lead Selection in Pediatric CIED MRI Safety Simulations

Hameed, S.; Henry, K.; Jiang, F.; Bhusal, B.; Dillenbeck, H.; Gakenheimer-Smith, L.; Webster, G.; Golestani Rad, L.

2026-05-30 radiology and imaging 10.64898/2026.05.26.26354162 medRxiv
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Pediatric patients with cardiac implantable electronic devices (CIEDs) face limited MRI access due to RF-induced heating, and computational modeling is increasingly used to characterize this risk. The validity of these simulations, however, depends on pairing body models with clinically realistic lead configurations, guidance that is currently lacking. We retrospectively analyzed 302 CIED surgeries in 281 pediatric patients to derive weight-based constraints for simulation design. Weight alone discriminated epicardial from endocardial lead implantation with AUC = 0.90, and adding age and height yielded no improvement, supporting weight as a sufficient single-parameter selection metric. The probabilistic crossover between approaches occurred at 44~kg, substantially higher than the 10 to 15~kg threshold commonly cited in the literature, with a broad transition zone of 21 to 66~kg in which both lead types were routinely used. Lead length was likewise weight-constrained: only 25~cm leads were observed in patients below 6~kg, and leads of 45~cm or longer were uncommon below 50~kg. These findings yield a three-tier framework, with epicardial-only configurations below 21~kg, dual configurations within 21 to 66~kg, and weight-thresholded lead lengths throughout, enabling MRI safety simulations to focus on clinically realizable anatomy and device combinations.

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TopBrain Segmentation Challenge for Whole Brain Vessel Anatomy

Yang, K.; Shi, P.; Huang, H.; Musio, F.; Baazaoui, H.; Aydin, O. U.; Hilbert, A.; Hamadache, R. E.; Yalcin, C.; Zhang, M.; Falcetta, D.; de la Rosa, E.; Shit, S.; Prabhakar, C.; Wittmann, B.; Rokuss, M. R.; Kirchhoff, Y.; Al-Maskari, R.; Hoeher, L.; Juchler, N.; Casamitjana, A.; Cleary, J.; Schmick, A.; Baumgartner, P.; Deseoe, J.; Vandans, O.; Lee, D.; Oh, K.; LaBella, D.; Mazher, M.; Niederer, S. A.; Qayyum, A.; Liu, Y.; Chen, J.; Kim, W.; Asawalertsak, N.; Kim, M.; Shin, D.; Park, S.-H.; Kikuchi, S.; Zhang, Y.; Liu, J.; Cui, Y.; Qiu, Y.; Verschuur, A.; Zhang, J.; van der Schaaf, I.; Su, R.;

2026-05-30 radiology and imaging 10.64898/2026.05.28.26354312 medRxiv
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We present the TopBrain 2025 Challenge, the first benchmark for fine-grained multiclass segmentation of the whole brain vasculature in both computed tomography angiography (CTA) and magnetic resonance angiography (MRA). Building on the TopCoW challenge, TopBrain scales vessel annotation from the Circle of Willis to the entire brain, introducing a dataset of 90 annotated volumes across 48 landmark vessel classes spanning arterial and venous systems, of which 50 training volumes are publicly released. Vessel definitions were consolidated from established neuroanatomical references into a unified annotation scheme, and vessel caliber measurements along the centerline are reported for the first time across the whole brain vascular anatomy. To address the unique challenges of multiclass brain vessel segmentation, we propose an evaluation framework that accounts for detection in segmentation performance, assesses anatomical plausibility, and introduces novel contamination metrics that characterize inter-class prediction errors. Fifteen teams from over 220 registered participants submitted algorithms to the benchmark. The top-performing teams built on nnUNet with principled system design choices, achieving around 80% Dice scores, near-zero invalid neighbor counts, over 60% F1 scores for side-road vessels, and below 18% foreground contamination ratio. Larger vessels are easier to segment, while smaller and more complex vessels remain the true bottleneck. The annotated datasets and podium-finish algorithms are made publicly available on Zenodo.

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PIE Toolbox: SSM-PCA Based Software for PET Diagnostic Pattern Analysis

Romanov, M.; Kireev, M.; Didur, M.; Cherednichenko, D.; Korotkov, A.; Valdes-Sosa, P.; Fan, Q.; Wang, Q.

2026-06-01 radiology and imaging 10.64898/2026.05.28.26354341 medRxiv
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One of the prominent methods in neuroimaging data processing is SSM-PCA, which is based on principal component analysis and allows for the identification of diagnostically significant patterns in the form of statistical maps. We developed software, PIE Toolbox, employs SSM-PCA and classification based on the obtained diagnostic patterns revealed from functional and structural tomographic brain imaging. The program supports the entire analysis pipeline including preprocessing of brain images, diagnostic patterns extraction, building classification models, and prediction based on them. The resulting diagnostic patterns are weighted principal components obtained through SSM-PCA, or their linear combinations. PIE Toolbox allows selection of relevant structural and functional brain patterns, computation of their expression values in regions of interest, classification using support vector machines, and evaluation of model performance via cross-validation. This approach enables the use of patterns as features of intergroup differences for individual diagnosis. The software has been validated on both simulated and ADNI datasets.

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Choroid plexus calcification detection using quantitative susceptibility mapping MRI

Hett, K.; Dubois, A.; Bonitz, I.; Considine, C. M.; Eaton, J.; Mcknight, C. D.; Claassen, D. O.; Donahue, M. J. J.; Trujillo, P.

2026-05-28 radiology and imaging 10.64898/2026.05.26.26354154 medRxiv
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Purpose. The choroid plexus (ChP) is the primary source of cerebrospinal fluid and an emerging marker of cerebral health, with enlargement and hypoperfusion reported in aging and neurodegeneration. However, frequent ChP calcifications can confound volumetric and perfusion measures. Although computed tomography (CT) is the gold standard for detecting calcification, it is rarely available in research MRI. Quantitative susceptibility mapping (QSM) offers an alternative sensitive to diamagnetic mineralization but lacks validated susceptibility thresholds. Method. Participants underwent CT and MRI within four weeks, including 3D T1-weighted and a multi-echo gradient echo QSM MRI. ChP calcifications were identified on CT using standard diagnostic criteria. Using the Bayes decision boundary framework, we identified optimal susceptibility thresholds for detecting diamagnetic signals consistent with calcification and compared these thresholds with multiple density levels measured on gold standard CT images. Results. Across all participants (n=20; age=62.2+-12.0 yrs), the optimal susceptibility threshold separating background ChP signal from calcifications was -0.10 ppm at 60 HU (low-density) and -0.15 ppm at 100 HU (high-density). Susceptibility values within calcified tissue exhibited a linear relationship with CT-derived tissue density. A significant positive association was observed between ChP volume and calcification volume among participants with detectable calcification (beta=2.26, p=0.047). Conclusion. This work should provide a practical framework for quantifying ChP calcifications routinely from MRI. The observed relationship between ChP volume and calcification volume highlights the importance of accounting for calcified tissue, particularly when calcification burden is substantial, when investigating ChP abnormalities in aging and neurodegenerative disease.

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Impact of AI-Assisted Mammography Reading on Quality Indicators in the Czech Breast Cancer Screening Programme: A Retrospective Study

Veverkova, L.; Dolezalova, Z.; Marackova, V.; Mathew, E.; Urbankova, M.; Ambrozova, M.; Piskovsky, T.; Ngo, O.; Majek, O.

2026-05-26 oncology 10.64898/2026.05.25.26353869 medRxiv
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Objectives: The aim of mammographic screening is the early detection of invasive cancers. In the era of artificial intelligence (AI), this tool may improve diagnosis of earlier stages. The purpose of this study was to assess the impact on selected quality indicators retrospectively. Method: The data source was the Breast Cancer Screening Registry using data from one Screening Unit that currently uses AI routinely. The indicators of the cancer detection rate (CDR), further assessment rate (FAR), and recall rate (RR) in the year 2023, when AI was used, and the year 2022, without AI, in women aged 45-69 were compared. The statistical evaluation used the chi-square test and logistic regression adjusting for the effects of age, a woman's risk level, and the screening round at a 5% significance level. Results: In 2022, without AI, 4,034 women aged 45-69 were included, compared with 4,049 women in 2023 when AI was used. This study showed a non-significant increase in CDR from 5.0 breast cancers detected per 1,000 women (non-AI assessment) to 5.2 (AI-assisted assessment), p = 0.919; OR (95% CI): 1.034 (0.542-1.974), a significant decrease in the FAR from 5.2% to 3.9%, p < 0.001; OR (95% CI): 0.665 (0.529-0.836), and a decrease in RR from 2.4% to 1.9%, p = 0.083; OR (95% CI): 0.754 (0.548-1.037). Conclusion: AI has the potential to be a useful tool in the early detection of breast cancer by improving quality through a decrease in FAR and RR, while probably maintaining CDR.

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Developing and Evaluating Deep Learning Approaches for Visual Field Denoising in Glaucoma

Baek, J. S.; Lokhande, A.; Neuenschwander, D.; Shi, M.; Wang, M.

2026-06-01 ophthalmology 10.64898/2026.05.29.26354019 medRxiv
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Purpose To investigate the relative efficacy of nine distinct visual field (VF) denoising artificial intelligence (AI) methods and a pathology-aware AI strategy to discourage over-correction of glaucomatous defects. Design Retrospective study. Participants 87,940 paired visual field (VF) and optical coherence tomography (OCT) samples from a tertiary academic center. Methods Denoising models were trained on a separate VF-only dataset and evaluated on an independent structure-function dataset of paired VF-OCT samples. We implemented and evaluated nine distinct VF denoising strategies representing three broad categories: baseline measurements, self-supervised and image restoration models (including Noise2Noise, Noise2Void, and NAFNet), and latent variable compression-based models (autoencoders and variational autoencoders). All models were designed to reconstruct VF sensitivity maps. We then predicted retinal nerve fiber layer thickness (RNFLT) maps from the denoised VFs using a fixed, independently trained VF-to-RNFLT prediction model. Main Outcome Measures Predicted VF and RNFLT maps and resultant evaluation metrics. Results The raw VF baseline achieved a global R2 of 0.5468 and MAE of 16.83 um. Restoration-based models maintained or slightly improved concordance, with the pathology-aware NAFNet achieving the highest global R2 of 0.5485 and a comparable MAE of 16.82 um. In contrast, compression-based models degraded concordance, with CNN-VAE showing a significant reduction (R2 approximately 0.50). In severe glaucoma, concordance decreased across all methods; however, compression architectures exhibited disproportionately greater degradation compared with restoration-based approaches. Conclusions We present a comparative benchmark of AI-based VF denoising strategies paired with structure-function evaluation. While restoration-based models can reduce variability without loss of biological signal, latent compression risks attenuating clinically meaningful defects. Visually smoother fields are not necessarily more biologically accurate.

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Automated quantification of cerebral microbleeds for ARIA-H monitoring in Aging and Alzheimer's Disease: A multicenter deep learning validation

Low, Z. X. B.; Rowsthorn, E.; Nazem-Zadeh, M.-R.; Francis, M.; Robb, C.; Howcroft, M.; Whiriskey, R.; Brodtmann, A.; McNeil, J. J.; Law, M.

2026-05-26 radiology and imaging 10.64898/2026.05.19.26353364 medRxiv
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We trained a self-configuring nnU-Net model for CMB segmentation in a heterogeneous multicenter sample (n=264), including 1.5T and 3T field strengths, SWI and T2*-GRE sequences, and community and clinical cohorts. Model performance was evaluated using 5-fold cross-validation with a focus on object-level detection metrics. Real-world performance was evaluated on scans from an unseen dataset of people with cerebrovascular disease (n=20). The model achieved 0.82 cluster Dice, 0.88 precision, and 0.77 sensitivity on hold-out test data. Notably, the model demonstrated a low false-positive rate, averaging 0.58 false positives (FPs) per scan, an improvement on existing publicly available models. The model achieved high performance in dataset of those with Alzheimer's disease and mild cognitive impairment (0.89 cluster Dice, 0.94 sensitivity), supporting its utility in clinical settings where ARIA-H monitoring is critical. In external validation, the model maintained high robustness with 0.79 sensitivity and 0.95 FPs per scan. By leveraging a heterogenous training strategy and a self-adapting architecture, we demonstrate that deep learning can achieve high-precision CMB detection that is robust to domain shifts. The low FP rate suggests this publicly available pipeline is suitable for automated screening and lesion counting in heterogenous large-scale clinical trials, reducing the burden of manual quantification.

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Optical coherence tomography as a biomarker for frontotemporal dementia: a systematic review & meta-analysis

Wang, E.; Kohli, A.; Taha, H. B.

2026-05-27 neurology 10.64898/2026.05.19.26353366 medRxiv
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Background: Frontotemporal dementia (FTD) lacks widely accessible disease-specific biomarkers. Optical coherence tomography (OCT) and OCT angiography (OCTA) may provide non-invasive measures of retinal changes associated with neurodegeneration. We conducted a systematic review and meta-analysis evaluating retinal biomarkers in FTD compared with Alzheimer disease (AD) and controls. Methods: A systematic search of PubMed and Embase was conducted through April 25, 2026 according to PRISMA guidelines. Studies evaluating OCT/OCTA biomarkers in FTD with comparator groups were included. Inverse weighted random-effects models, publication bias assessments, and meta-regressions were performed. Results: Ten studies involving 139 individuals with FTD, 87 with AD, 29 with mild cognitive impairment, 14 with TDP-43 proteinopathy, 5 with tauopathy, and 255 controls were included in the systematic review; five studies were eligible for meta-analysis. Compared with AD, individuals with FTD demonstrated significantly thinner retinal nerve fiber layer (RNFL) thickness (SMD = -0.61, 95% CI -0.98, -0.24). Compared with controls, individuals with FTD exhibited significantly thinner ganglion cell layer-inner plexiform layer (GCL-IPL) thickness (SMD = -0.55, 95% CI -1.02, -0.08), whereas pooled analyses across multiple retinal biomarkers were non-significant (SMD = -0.19, 95% CI -0.52, 0.14). RNFL thickness correlated negatively with female % in FTD and positively with age in both AD and controls. Conclusions: Individuals with FTD exhibit lower RNFL thickness than AD and lower GCL-IPL thickness than controls, suggesting retinal alterations may reflect neurodegeneration. However, larger longitudinal studies with standardized OCT/OCTA protocols are needed to determine the diagnostic and prognostic utility of retinal biomarkers in FTD

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Auditable cross-instrument detection of unusual multivariate psychiatric response configurations using a semantically aligned covariance subspace

Periwal, V.

2026-05-27 psychiatry and clinical psychology 10.64898/2026.05.22.26353902 medRxiv
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Background: Conventional psychiatric screening instruments summarize symptoms within individual scales and prioritize cases with high single-instrument additive score severity. This design treats items as independent within instruments and ignores cross-instrument covariance structure, making it insensitive to respondents whose responses are distributed across multiple domains in unusual combinations that remain below threshold on every individual scale. Methods: We analyzed two cohorts spanning older and younger adults. Item prompts from depression, stress, anxiety, and sleep instruments were embedded into a shared semantic space using a pretrained sentence encoder. Principal component analysis of the item-prompt embeddings alone---with no use of respondent data at this stage---was used to construct a low-dimensional subspace retaining 80\% of variance in the item embedding matrix. Normalized participant responses were then projected into this subspace, with Jaccard-based stability analysis used as a check on dimensional robustness. Multivariate deviation from the cohort norm was quantified with Mahalanobis distance using Ledoit-Wolf covariance regularization. Candidate outliers were defined by the empirical 95th percentile of the cohort-specific distance distribution. To isolate response configurations not already captured by conventional single-instrument extreme-value logic, we excluded all outlier respondents who had endorsed any individual item at the maximum value of its Likert scale on any instrument. For the remaining outliers, anomalous components were backtracked to their original item loadings for interpretation. Results: In the older-adult Health and Retirement Study (HRS) cohort, principal component analysis of 27 item-prompt embeddings showed that a 10-dimensional subspace provided a stable representation of cross-instrument semantic structure. In the younger-adult Xinxiang cohort the corresponding stable solution was 16-dimensional. In each cohort, seven respondents remained as multivariate outliers despite falling below every single-instrument extreme-value threshold. These cases were not characterized by uniformly severe symptom scores but by unusual cross-domain response configurations that became visible only in the shared semantic covariance subspace. The response structure of the retained configurations differed across cohorts: older-adult cases more often involved weak endorsement of mood-labeled items alongside nonzero body- and sleep-related responses, whereas younger-adult cases more often involved incomplete response configurations spanning mood, sleep, stress, and self-harm-related items. Conclusions: A semantically aligned, auditable covariance subspace provides a practical tool for flagging unusual multivariate response configurations that single-instrument additive screening may not flag. The method is interpretable at the level of original item contributions. It should be understood as a hypothesis-generating screen for unusual response configurations requiring further clinical assessment, not as a diagnostic instrument. Outcome validity remains to be established by prospective study.

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Data Assimilation Substitutes for Biological Complexity in Hybrid Influenza Forecasting Models

Alleman, T. W.; Van Wesemael, T.; Shanker, N.; Mietchen, M. S.; Loo, S.; Ajagbe, S. O.; Baetens, J. M.; Lemaitre, J.; Hill, A. L.; Truelove, S. A.; Bento, A. I.

2026-05-27 public and global health 10.64898/2026.05.19.26353597 medRxiv
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Hybrid mechanistic-statistical models offer interpretability and adaptability for short-term seasonal epidemic forecasting, but it remains unclear whether their accuracy depends more on increased biological complexity or on the assimilation of richer data. Using eight retrospective influenza seasons in North Carolina, we evaluate whether training on historical data and assimilating auxiliary emergency department (ED) visit data improves four-week-ahead hospital admission forecasts more than adding biological complexity (multi-subtype structure and cross-season immunity). Hierarchical Bayesian training on historical data improves accuracy by 22.4 % (95 % CI: 16.4-28.1 %), and inclusion of ED visit data yields a further 5.3 % (95 % CI: 3.0-7.6 %) improvement, whereas added biological complexity produces diminishing or null gains. We further observe a substitution effect in which ED visit data partially compensates for omitted biological structure. We deployed a simplified model variant in the 2025-2026 CDC FluSight Challenge and ranked among the top ensemble performers, supporting the robustness of Bayesian hierarchical training in real time. Together, these findings indicate that short-term forecast accuracy is driven more by historical learning and assimilating auxiliary signals than by biological fidelity, with implications for how forecasting systems should balance mechanistic complexity.