arXiv subjects

Julia F. Lehman

Publications and source records attributed to Julia F. Lehman.

4 recordsLinked to original sources

arXiv2026

Topology-Aware Training and Spatial Diagnostics for Fiber Bundle Segmentation in Tracer Histology

Anatomic tracer studies reveal how axon bundles project from an injection site, branch into smaller groups of axons, and course through the brain to reach their destinations. Histological data from such studies provide anatomical reference information for validating diffusion MRI tractography. However, manual annotation of the histological data is very labor-intensive, and although automated segmentation methods have been proposed, they rely mainly on pixel-overlap losses such as BCE and Dice; topology-aware loss functions have not been studied for this task. We compare BCE-Dice, clDice, Betti matching, and Topograph for fiber bundle segmentation in macaque tracer histology using a frozen DINOv3 backbone. To our knowledge, this is the first exploration of foundation-model features for this task. BCE-Dice achieved the highest Dice, while clDice achieved the highest bundle recall but poor mask overlap. Topograph had similar Dice to BCE-Dice, the lowest $β_0$ error, and fewer false positives than BCE-Dice and Betti matching. Fiber bundle segmentation methods are typically evaluated with a permissive rule that counts a bundle as detected given any overlap with the prediction. We show this rule does not capture oversegmentation, and that per-section TPR can be inflated by empty sections assigned perfect recall. To quantify this, we introduce Excess32, a spatial diagnostic measuring predicted pixels outside a 32-pixel tolerance band around annotated bundles. In validation, a Betti-Topograph union raises sparse-bundle TPR from 0.818 to 0.933, but worsens FDR from 0.296 to 0.509, Excess32 from 0.108 to 0.466, and area ratio from 0.94 to 3.34. These results show detection metrics alone are insufficient to characterize segmentation quality.

cs.CV↗

arXiv2026

Tractography-Driven Synthetic Data Generation for Fiber Bundle Segmentation in Tracer Histology

Diffusion MRI (dMRI) tractography enables non-invasive reconstruction of white-matter pathways, but its accuracy is fundamentally limited by indirect, low-resolution measurements of axonal organization. Tracer injection studies in non-human primates provide a gold standard for validating dMRI tractography. This, however, requires time-consuming manual annotation of fiber bundles in histology sections. We propose a synthetic-data augmented framework for automated fiber bundle segmentation in macaque tracer histology. Our approach uses ex vivo dMRI tractography as a generative prior to synthesize 2D image patches for training. This provides us with sufficiently realistic foreground texture, which we compose with backgrounds from blockface photos and diversify via domain randomization. A 2D U-Net is trained on mixed real and synthetic patches. Experiments on held-out brains demonstrate improved generalization across brains and fiber bundle densities compared to training with real data only. Training with synthetic data only leads to poor performance, underscoring the need for real supervision. Overall, our approach achieves performance comparable to the state-of-the-art while requiring 3x less manually annotated data.

cs.CV↗

arXiv2025

Fully Automated Segmentation of Fiber Bundles in Anatomic Tracing Data

Anatomic tracer studies are critical for validating and improving diffusion MRI (dMRI) tractography. However, large-scale analysis of data from such studies is hampered by the labor-intensive process of annotating fiber bundles manually on histological slides. Existing automated methods often miss sparse bundles or require complex post-processing across consecutive sections, limiting their flexibility and generalizability. We present a streamlined, fully automated framework for fiber bundle segmentation in macaque tracer data, based on a U-Net architecture with large patch sizes, foreground aware sampling, and semisupervised pre-training. Our approach eliminates common errors such as mislabeling terminals as bundles, improves detection of sparse bundles by over 20% and reduces the False Discovery Rate (FDR) by 40% compared to the state-of-the-art, all while enabling analysis of standalone slices. This new framework will facilitate the automated analysis of anatomic tracing data at a large scale, generating more ground-truth data that can be used to validate and optimize dMRI tractography methods.

cs.CV↗

arXiv2022

Constrained self-supervised method with temporal ensembling for fiber bundle detection on anatomic tracing data

Anatomic tracing data provides detailed information on brain circuitry essential for addressing some of the common errors in diffusion MRI tractography. However, automated detection of fiber bundles on tracing data is challenging due to sectioning distortions, presence of noise and artifacts and intensity/contrast variations. In this work, we propose a deep learning method with a self-supervised loss function that takes anatomy-based constraints into account for accurate segmentation of fiber bundles on the tracer sections from macaque brains. Also, given the limited availability of manual labels, we use a semi-supervised training technique for efficiently using unlabeled data to improve the performance, and location constraints for further reduction of false positives. Evaluation of our method on unseen sections from a different macaque yields promising results with a true positive rate of ~0.90. The code for our method is available at https://github.com/v-sundaresan/fiberbundle_seg_tracing.

eess.IV↗