LoRCA: LoRA Cycle Adaptation for Histology to HiP-CT Translation with DINOv3
Authors: Yang Zhou, Edoardo Occhipinti, Banboye Kidzeru Elvis, Jishizhan Chen, Stathis Megas, Joseph Brunet, Joanna Purzycka, Theresa Urban, +6 more
Abstract
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 (∼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.
Three-dimensional (3D) histopathology of unprocessed tissues has the potential to transform disease management by enabling volumetric characterization of tissue microarchitecture and in-vivo assessment. Back-illumination Interference Tomography (BIT) is a new phase microscopy technology that provides rapid, non-destructive volumetric imaging of unprocessed tissues. However, translating BIT volumes into clinically interpretable H&E images remains challenging, particularly due to shift-variant contrast and the absence of quantitative validation benchmarks. We introduce HistoBIT3D, the first voxel-wise paired BIT and fluorescence-labeled nuclei dataset, enabling quantitative evaluation of structural preservation in unsupervised virtual staining against ground-truth nuclear distributions. Using this dataset, we present a novel virtual staining framework that translates BIT volumes with shift-variant contrast into realistic H&E volumes by leveraging bidirectional multiscale content consistency and cross-domain style reuse to enhance structural fidelity and perceptual realism. Our method achieves state-of-the-art realism metrics while significantly improving 3D nuclei segmentation accuracy and boundary preservation under zero-shot Cellpose evaluation. Together, these contributions establish a quantitatively validated, structurally faithful, and scalable pipeline for 3D virtual H&E staining, advancing the paradigm of slide-free, volumetric computational histopathology. Our data and code are available at: https://github.com/aasong113/HistoBIT3D_VirtualStaining.
CT vision-language foundation models have demonstrated promising performance across downstream tasks, but are typically trained with whole-volume representations that dilute fine-grained anatomical signals. Fine-grained vision-language pre-training addresses this by aligning anatomy-level visual features with anatomy-specific text, but in doing so discards the global context that whole-volume models provide. Furthermore, existing fine-grained approaches train from scratch, making them computationally expensive. We introduce Anatomy Contextualized Adaptation (ACA), a lightweight framework that adapts frozen CT foundation model representations for anatomy-level vision-language alignment while enhancing global contextualization. ACA uses TotalSegmentator to decompose CT volumes into anatomy-level embeddings, which are refined via a transformer that captures cross-anatomy relationships, and aligned to both per-anatomy and scan-level text extracted from radiology reports. Evaluated on Merlin and CT-RATE, ACA consistently outperforms both the frozen foundation model baselines and existing fine-grained methods in zero-shot finding classification, while requiring less than one hour of training once embeddings are cached. The attention weights learned by ACA's inter-anatomy transformer additionally indicate plausible cross-anatomy context routing. Altogether, these results support ACA as a lightweight approach for adapting CT foundation models to anatomically grounded vision-language alignment while preserving and enhancing global anatomical context.
Roshan Kenia, Stephanie L McNamara, William Lotter
Learning transferable representations from CT-report pairs requires combining whole-volume context with anatomy-specific evidence. Existing methods typically emphasize either global CT-report alignment or fine-grained anatomy-level correspondence. Global alignment preserves broad study context but leaves the contribution of localized evidence implicit, whereas anatomy-level alignment explicitly grounds local findings but does not specify how independently represented evidence should interact, acquire study-level meaning, and contribute to a global CT representation. To address this gap, we propose SCOPE (Semantic Calibration Of comPosed Evidence), a framework for semantically calibrated evidence composition in CT vision-language learning. Under organ-specific report supervision, mask-guided queries with fixed anatomical identities extract context-aware organ evidence from shared, uncropped volumetric features, while an unrestricted global query retains access to whole-volume context. The global query then drives Local-Global Coupling to compose the organ evidence into a unified evidence representation. The composed evidence is subsequently calibrated using the diagnostic summary, providing study-level semantic supervision beyond local organ descriptions, and is finally integrated as a controlled residual into a context-preserving whole-volume representation aligned with the complete report. This progressive pathway connects localized evidence with study-level semantics without reducing the CT representation to a predefined set of organs. On CT-RATE and RadChestCT, SCOPE achieves macro AUCs of 85.0 and 72.2, respectively, outperforming the previous SOTA by 7.2 and 4.2, while also yielding substantial gains in linear probing and cross-modal retrieval. These results demonstrate the effectiveness of semantically calibrated evidence composition.