Neurovascular Segmentation in sOCT with Deep Learning and Synthetic Training Data

Microvascular anatomy is known to be involved in various neurological disorders. However, understanding these disorders is hindered by the lack of imaging modalities capable of capturing the comprehensive three-dimensional vascular network structure at microscopic resolution. With a lateral resolution of $<=$20 {\textmu}m and ability to reconstruct large tissue blocks up to tens of cubic centimeters, serial-section optical coherence tomography (sOCT) is well suited for this task. This method uses intrinsic optical properties to visualize the vessels and therefore does not possess a specific contrast, which complicates the extraction of accurate vascular models. The performance of traditional vessel segmentation methods is heavily degraded in the presence of substantial noise and imaging artifacts and is sensitive to domain shifts, while convolutional neural networks (CNNs) require extensive labeled data and are also sensitive the precise intensity characteristics of the data that they are trained on. Building on the emerging field of synthesis-based training, this study demonstrates a synthesis engine for neurovascular segmentation in sOCT images. Characterized by minimal priors and high variance sampling, our highly generalizable method tested on five distinct sOCT acquisitions eliminates the need for manual annotations while attaining human-level precision. Our approach comprises two phases: label synthesis and label-to-image transformation. We demonstrate the efficacy of the former by comparing it to several more realistic sets of training labels, and the latter by an ablation study of synthetic noise and artifact models.

A label-free and data-free training strategy for vasculature segmentation in serial sectioning OCT data

Serial sectioning Optical Coherence Tomography (sOCT) is a high-throughput, label free microscopic imaging technique that is becoming increasingly popular to study post-mortem neurovasculature. Quantitative analysis of the vasculature requires highly accurate segmentation; however, sOCT has low signal-to-noise-ratio and displays a wide range of contrasts and artifacts that depend on acquisition parameters. Furthermore, labeled data is scarce and extremely time consuming to generate. Here, we leverage synthetic datasets of vessels to train a deep learning segmentation model. We construct the vessels with semi-realistic splines that simulate the vascular geometry and compare our model with realistic vascular labels generated by constrained constructive optimization. Both approaches yield similar Dice scores, although with very different false positive and false negative rates. This method addresses the complexity inherent in OCT images and paves the way for more accurate and efficient analysis of neurovascular structures.

Uncertainty-Aware Annotation Protocol to Evaluate Deformable Registration Algorithms

Landmark correspondences are a widely used type of gold standard in image registration. However, the manual placement of corresponding points is subject to high inter-user variability in the chosen annotated locations and in the interpretation of visual ambiguities. In this paper, we introduce a principled strategy for the construction of a gold standard in deformable registration. Our framework: (i) iteratively suggests the most informative location to annotate next, taking into account its redundancy with previous annotations; (ii) extends traditional pointwise annotations by accounting for the spatial uncertainty of each annotation, which can either be directly specified by the user, or aggregated from pointwise annotations from multiple experts; and (iii) naturally provides a new strategy for the evaluation of deformable registration algorithms. Our approach is validated on four different registration tasks. The experimental results show the efficacy of suggesting annotations according to their informativeness, and an improved capacity to assess the quality of the outputs of registration algorithms. In addition, our approach yields, from sparse annotations only, a dense visualization of the errors made by a registration method. The source code of our approach supporting both 2D and 3D data is publicly available at https://github.com/LoicPeter/evaluation-deformable-registration.