LoRCA: LoRA Cycle Adaptation for Histology to HiP-CT Translation with DINOv3

Hierarchical Phase-Contrast Tomography (HiP-CT) is a synchrotron based X-ray imaging technique that enables non-destructive, volumetric imaging of intact organs with multi-resolutions bridging 20 $μm$/voxel for whole organs to near-cellular resolution ($\sim$0.8 $μm$/voxel) in local regions. This offers the opportunity to bring volumetric whole-organ context to histology. However, nonlinear registration between H\&E histology and HiP-CT volumes is challenging due to the differences in feature representations of different colour spaces. Synthesis-before-registration methods have shown strong results in histology-to-MRI and histology-to-CT alignment. However, existing approaches either rely on manual anatomical contours or are trained from scratch without semantic constraints, limiting their generalisability to soft tissue organs and novel modalities. We propose LoRCA (LoRA Cycle Adaptation), a cycle consistent style translation framework built on a shared frozen DINOv3 with modality-specific LoRA adapters, learning modality-specific representations that are decoded and adversarially trained. LoRCA enables structure-preserving translation without requiring paired training data. The frozen backbone is intended to be a structural anchor that prevents content drift by preserving pretrained semantic-extraction capability. We evaluate translation quality using Fréchet Inception Distance (FID) and structural fidelity via mutual information and Canny edge preservation. LoRCA outperforms CycleGAN in both translation quality and structural consistency. As a preliminary indicator of downstream registration utility, we find that style-translated images yield increased feature correspondences under MatchAnything on manually aligned HiP-CT and histology test pairs, suggesting that LoRCA-style translation is a promising step towards 2D histological sections to 3D HiP-CT volumes registration.

Deep Learning for Vascular Segmentation and Applications in Phase Contrast Tomography Imaging

Automated blood vessel segmentation is vital for biomedical imaging, as vessel changes indicate many pathologies. Still, precise segmentation is difficult due to the complexity of vascular structures, anatomical variations across patients, the scarcity of annotated public datasets, and the quality of images. We present a thorough literature review, highlighting the state of machine learning techniques across diverse organs. Our goal is to provide a foundation on the topic and identify a robust baseline model for application to vascular segmentation in a new imaging modality, Hierarchical Phase Contrast Tomography (HiP CT). Introduced in 2020 at the European Synchrotron Radiation Facility, HiP CT enables 3D imaging of complete organs at an unprecedented resolution of ca. 20mm per voxel, with the capability for localized zooms in selected regions down to 1mm per voxel without sectioning. We have created a training dataset with double annotator validated vascular data from three kidneys imaged with HiP CT in the context of the Human Organ Atlas Project. Finally, utilising the nnU Net model, we conduct experiments to assess the models performance on both familiar and unseen samples, employing vessel specific metrics. Our results show that while segmentations yielded reasonably high scores such as clDice values ranging from 0.82 to 0.88, certain errors persisted. Large vessels that collapsed due to the lack of hydrostatic pressure (HiP CT is an ex vivo technique) were segmented poorly. Moreover, decreased connectivity in finer vessels and higher segmentation errors at vessel boundaries were observed. Such errors obstruct the understanding of the structures by interrupting vascular tree connectivity. Through our review and outputs, we aim to set a benchmark for subsequent model evaluations using various modalities, especially with the HiP CT imaging database.