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Tom Vercauteren

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Unified Brain MR-Ultrasound Synthesis using Multi-Modal Hierarchical Representations

Sep 19, 2023
Reuben Dorent, Nazim Haouchine, Fryderyk Kögl, Samuel Joutard, Parikshit Juvekar, Erickson Torio, Alexandra Golby, Sebastien Ourselin, Sarah Frisken, Tom Vercauteren, Tina Kapur, William M. Wells

We introduce MHVAE, a deep hierarchical variational auto-encoder (VAE) that synthesizes missing images from various modalities. Extending multi-modal VAEs with a hierarchical latent structure, we introduce a probabilistic formulation for fusing multi-modal images in a common latent representation while having the flexibility to handle incomplete image sets as input. Moreover, adversarial learning is employed to generate sharper images. Extensive experiments are performed on the challenging problem of joint intra-operative ultrasound (iUS) and Magnetic Resonance (MR) synthesis. Our model outperformed multi-modal VAEs, conditional GANs, and the current state-of-the-art unified method (ResViT) for synthesizing missing images, demonstrating the advantage of using a hierarchical latent representation and a principled probabilistic fusion operation. Our code is publicly available \url{}.

* Accepted at MICCAI 2023 
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UPL-SFDA: Uncertainty-aware Pseudo Label Guided Source-Free Domain Adaptation for Medical Image Segmentation

Sep 19, 2023
Jianghao Wu, Guotai Wang, Ran Gu, Tao Lu, Yinan Chen, Wentao Zhu, Tom Vercauteren, Sébastien Ourselin, Shaoting Zhang

Domain Adaptation (DA) is important for deep learning-based medical image segmentation models to deal with testing images from a new target domain. As the source-domain data are usually unavailable when a trained model is deployed at a new center, Source-Free Domain Adaptation (SFDA) is appealing for data and annotation-efficient adaptation to the target domain. However, existing SFDA methods have a limited performance due to lack of sufficient supervision with source-domain images unavailable and target-domain images unlabeled. We propose a novel Uncertainty-aware Pseudo Label guided (UPL) SFDA method for medical image segmentation. Specifically, we propose Target Domain Growing (TDG) to enhance the diversity of predictions in the target domain by duplicating the pre-trained model's prediction head multiple times with perturbations. The different predictions in these duplicated heads are used to obtain pseudo labels for unlabeled target-domain images and their uncertainty to identify reliable pseudo labels. We also propose a Twice Forward pass Supervision (TFS) strategy that uses reliable pseudo labels obtained in one forward pass to supervise predictions in the next forward pass. The adaptation is further regularized by a mean prediction-based entropy minimization term that encourages confident and consistent results in different prediction heads. UPL-SFDA was validated with a multi-site heart MRI segmentation dataset, a cross-modality fetal brain segmentation dataset, and a 3D fetal tissue segmentation dataset. It improved the average Dice by 5.54, 5.01 and 6.89 percentage points for the three tasks compared with the baseline, respectively, and outperformed several state-of-the-art SFDA methods.

* 12 pages, 6 figures, to be published on IEEE TMI 
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MedShapeNet -- A Large-Scale Dataset of 3D Medical Shapes for Computer Vision

Sep 12, 2023
Jianning Li, Antonio Pepe, Christina Gsaxner, Gijs Luijten, Yuan Jin, Narmada Ambigapathy, Enrico Nasca, Naida Solak, Gian Marco Melito, Viet Duc Vu, Afaque R. Memon, Xiaojun Chen, Jan Stefan Kirschke, Ezequiel de la Rosa, Patrick Ferdinand Christ, Hongwei Bran Li, David G. Ellis, Michele R. Aizenberg, Sergios Gatidis, Thomas Küstner, Nadya Shusharina, Nicholas Heller, Vincent Andrearczyk, Adrien Depeursinge, Mathieu Hatt, Anjany Sekuboyina, Maximilian Löffler, Hans Liebl, Reuben Dorent, Tom Vercauteren, Jonathan Shapey, Aaron Kujawa, Stefan Cornelissen, Patrick Langenhuizen, Achraf Ben-Hamadou, Ahmed Rekik, Sergi Pujades, Edmond Boyer, Federico Bolelli, Costantino Grana, Luca Lumetti, Hamidreza Salehi, Jun Ma, Yao Zhang, Ramtin Gharleghi, Susann Beier, Arcot Sowmya, Eduardo A. Garza-Villarreal, Thania Balducci, Diego Angeles-Valdez, Roberto Souza, Leticia Rittner, Richard Frayne, Yuanfeng Ji, Soumick Chatterjee, Florian Dubost, Stefanie Schreiber, Hendrik Mattern, Oliver Speck, Daniel Haehn, Christoph John, Andreas Nürnberger, João Pedrosa, Carlos Ferreira, Guilherme Aresta, António Cunha, Aurélio Campilho, Yannick Suter, Jose Garcia, Alain Lalande, Emmanuel Audenaert, Claudia Krebs, Timo Van Leeuwen, Evie Vereecke, Rainer Röhrig, Frank Hölzle, Vahid Badeli, Kathrin Krieger, Matthias Gunzer, Jianxu Chen, Amin Dada, Miriam Balzer, Jana Fragemann, Frederic Jonske, Moritz Rempe, Stanislav Malorodov, Fin H. Bahnsen, Constantin Seibold, Alexander Jaus, Ana Sofia Santos, Mariana Lindo, André Ferreira, Victor Alves, Michael Kamp, Amr Abourayya, Felix Nensa, Fabian Hörst, Alexander Brehmer, Lukas Heine, Lars E. Podleska, Matthias A. Fink, Julius Keyl, Konstantinos Tserpes, Moon-Sung Kim, Shireen Elhabian, Hans Lamecker, Dženan Zukić, Beatriz Paniagua, Christian Wachinger, Martin Urschler, Luc Duong, Jakob Wasserthal, Peter F. Hoyer, Oliver Basu, Thomas Maal, Max J. H. Witjes, Ti-chiun Chang, Seyed-Ahmad Ahmadi, Ping Luo, Bjoern Menze, Mauricio Reyes, Christos Davatzikos, Behrus Puladi, Jens Kleesiek, Jan Egger

We present MedShapeNet, a large collection of anatomical shapes (e.g., bones, organs, vessels) and 3D surgical instrument models. Prior to the deep learning era, the broad application of statistical shape models (SSMs) in medical image analysis is evidence that shapes have been commonly used to describe medical data. Nowadays, however, state-of-the-art (SOTA) deep learning algorithms in medical imaging are predominantly voxel-based. In computer vision, on the contrary, shapes (including, voxel occupancy grids, meshes, point clouds and implicit surface models) are preferred data representations in 3D, as seen from the numerous shape-related publications in premier vision conferences, such as the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), as well as the increasing popularity of ShapeNet (about 51,300 models) and Princeton ModelNet (127,915 models) in computer vision research. MedShapeNet is created as an alternative to these commonly used shape benchmarks to facilitate the translation of data-driven vision algorithms to medical applications, and it extends the opportunities to adapt SOTA vision algorithms to solve critical medical problems. Besides, the majority of the medical shapes in MedShapeNet are modeled directly on the imaging data of real patients, and therefore it complements well existing shape benchmarks comprising of computer-aided design (CAD) models. MedShapeNet currently includes more than 100,000 medical shapes, and provides annotations in the form of paired data. It is therefore also a freely available repository of 3D models for extended reality (virtual reality - VR, augmented reality - AR, mixed reality - MR) and medical 3D printing. This white paper describes in detail the motivations behind MedShapeNet, the shape acquisition procedures, the use cases, as well as the usage of the online shape search portal:

* 21 pages 
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DEEPBEAS3D: Deep Learning and B-Spline Explicit Active Surfaces

Sep 05, 2023
Helena Williams, João Pedrosa, Muhammad Asad, Laura Cattani, Tom Vercauteren, Jan Deprest, Jan D'hooge

Deep learning-based automatic segmentation methods have become state-of-the-art. However, they are often not robust enough for direct clinical application, as domain shifts between training and testing data affect their performance. Failure in automatic segmentation can cause sub-optimal results that require correction. To address these problems, we propose a novel 3D extension of an interactive segmentation framework that represents a segmentation from a convolutional neural network (CNN) as a B-spline explicit active surface (BEAS). BEAS ensures segmentations are smooth in 3D space, increasing anatomical plausibility, while allowing the user to precisely edit the 3D surface. We apply this framework to the task of 3D segmentation of the anal sphincter complex (AS) from transperineal ultrasound (TPUS) images, and compare it to the clinical tool used in the pelvic floor disorder clinic (4D View VOCAL, GE Healthcare; Zipf, Austria). Experimental results show that: 1) the proposed framework gives the user explicit control of the surface contour; 2) the perceived workload calculated via the NASA-TLX index was reduced by 30% compared to VOCAL; and 3) it required 7 0% (170 seconds) less user time than VOCAL (p< 0.00001)

* 4 pages, 3 figures, 1 table, conference 
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Privileged Anatomical and Protocol Discrimination in Trackerless 3D Ultrasound Reconstruction

Aug 20, 2023
Qi Li, Ziyi Shen, Qian Li, Dean C. Barratt, Thomas Dowrick, Matthew J. Clarkson, Tom Vercauteren, Yipeng Hu

Three-dimensional (3D) freehand ultrasound (US) reconstruction without using any additional external tracking device has seen recent advances with deep neural networks (DNNs). In this paper, we first investigated two identified contributing factors of the learned inter-frame correlation that enable the DNN-based reconstruction: anatomy and protocol. We propose to incorporate the ability to represent these two factors - readily available during training - as the privileged information to improve existing DNN-based methods. This is implemented in a new multi-task method, where the anatomical and protocol discrimination are used as auxiliary tasks. We further develop a differentiable network architecture to optimise the branching location of these auxiliary tasks, which controls the ratio between shared and task-specific network parameters, for maximising the benefits from the two auxiliary tasks. Experimental results, on a dataset with 38 forearms of 19 volunteers acquired with 6 different scanning protocols, show that 1) both anatomical and protocol variances are enabling factors for DNN-based US reconstruction; 2) learning how to discriminate different subjects (anatomical variance) and predefined types of scanning paths (protocol variance) both significantly improve frame prediction accuracy, volume reconstruction overlap, accumulated tracking error and final drift, using the proposed algorithm.

* Accepted to Advances in Simplifying Medical UltraSound (ASMUS) workshop at MICCAI 2023 
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SegMatch: A semi-supervised learning method for surgical instrument segmentation

Aug 09, 2023
Meng Wei, Charlie Budd, Luis C. Garcia-Peraza-Herrera, Reuben Dorent, Miaojing Shi, Tom Vercauteren

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Surgical instrument segmentation is recognised as a key enabler to provide advanced surgical assistance and improve computer assisted interventions. In this work, we propose SegMatch, a semi supervised learning method to reduce the need for expensive annotation for laparoscopic and robotic surgical images. SegMatch builds on FixMatch, a widespread semi supervised classification pipeline combining consistency regularization and pseudo labelling, and adapts it for the purpose of segmentation. In our proposed SegMatch, the unlabelled images are weakly augmented and fed into the segmentation model to generate a pseudo-label to enforce the unsupervised loss against the output of the model for the adversarial augmented image on the pixels with a high confidence score. Our adaptation for segmentation tasks includes carefully considering the equivariance and invariance properties of the augmentation functions we rely on. To increase the relevance of our augmentations, we depart from using only handcrafted augmentations and introduce a trainable adversarial augmentation strategy. Our algorithm was evaluated on the MICCAI Instrument Segmentation Challenge datasets Robust-MIS 2019 and EndoVis 2017. Our results demonstrate that adding unlabelled data for training purposes allows us to surpass the performance of fully supervised approaches which are limited by the availability of training data in these challenges. SegMatch also outperforms a range of state-of-the-art semi-supervised learning semantic segmentation models in different labelled to unlabelled data ratios.

* preprint under review, 12 pages, 7 figures 
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Deep Homography Prediction for Endoscopic Camera Motion Imitation Learning

Jul 24, 2023
Martin Huber, Sebastien Ourselin, Christos Bergeles, Tom Vercauteren

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In this work, we investigate laparoscopic camera motion automation through imitation learning from retrospective videos of laparoscopic interventions. A novel method is introduced that learns to augment a surgeon's behavior in image space through object motion invariant image registration via homographies. Contrary to existing approaches, no geometric assumptions are made and no depth information is necessary, enabling immediate translation to a robotic setup. Deviating from the dominant approach in the literature which consist of following a surgical tool, we do not handcraft the objective and no priors are imposed on the surgical scene, allowing the method to discover unbiased policies. In this new research field, significant improvements are demonstrated over two baselines on the Cholec80 and HeiChole datasets, showcasing an improvement of 47% over camera motion continuation. The method is further shown to indeed predict camera motion correctly on the public motion classification labels of the AutoLaparo dataset. All code is made accessible on GitHub.

* Early accepted at MICCAI 2023 
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Synthetic white balancing for intra-operative hyperspectral imaging

Jul 24, 2023
Anisha Bahl, Conor C. Horgan, Mirek Janatka, Oscar J. MacCormac, Philip Noonan, Yijing Xie, Jianrong Qiu, Nicola Cavalcanti, Philipp Fürnstahl, Michael Ebner, Mads S. Bergholt, Jonathan Shapey, Tom Vercauteren

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Hyperspectral imaging shows promise for surgical applications to non-invasively provide spatially-resolved, spectral information. For calibration purposes, a white reference image of a highly-reflective Lambertian surface should be obtained under the same imaging conditions. Standard white references are not sterilizable, and so are unsuitable for surgical environments. We demonstrate the necessity for in situ white references and address this by proposing a novel, sterile, synthetic reference construction algorithm. The use of references obtained at different distances and lighting conditions to the subject were examined. Spectral and color reconstructions were compared with standard measurements qualitatively and quantitatively, using $\Delta E$ and normalised RMSE respectively. The algorithm forms a composite image from a video of a standard sterile ruler, whose imperfect reflectivity is compensated for. The reference is modelled as the product of independent spatial and spectral components, and a scalar factor accounting for gain, exposure, and light intensity. Evaluation of synthetic references against ideal but non-sterile references is performed using the same metrics alongside pixel-by-pixel errors. Finally, intraoperative integration is assessed though cadaveric experiments. Improper white balancing leads to increases in all quantitative and qualitative errors. Synthetic references achieve median pixel-by-pixel errors lower than 6.5% and produce similar reconstructions and errors to an ideal reference. The algorithm integrated well into surgical workflow, achieving median pixel-by-pixel errors of 4.77%, while maintaining good spectral and color reconstruction.

* 22 pages, 10 figures 
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Deep Reinforcement Learning Based System for Intraoperative Hyperspectral Video Autofocusing

Jul 21, 2023
Charlie Budd, Jianrong Qiu, Oscar MacCormac, Martin Huber, Christopher Mower, Mirek Janatka, Théo Trotouin, Jonathan Shapey, Mads S. Bergholt, Tom Vercauteren

Figure 1 for Deep Reinforcement Learning Based System for Intraoperative Hyperspectral Video Autofocusing
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Hyperspectral imaging (HSI) captures a greater level of spectral detail than traditional optical imaging, making it a potentially valuable intraoperative tool when precise tissue differentiation is essential. Hardware limitations of current optical systems used for handheld real-time video HSI result in a limited focal depth, thereby posing usability issues for integration of the technology into the operating room. This work integrates a focus-tunable liquid lens into a video HSI exoscope, and proposes novel video autofocusing methods based on deep reinforcement learning. A first-of-its-kind robotic focal-time scan was performed to create a realistic and reproducible testing dataset. We benchmarked our proposed autofocus algorithm against traditional policies, and found our novel approach to perform significantly ($p<0.05$) better than traditional techniques ($0.070\pm.098$ mean absolute focal error compared to $0.146\pm.148$). In addition, we performed a blinded usability trial by having two neurosurgeons compare the system with different autofocus policies, and found our novel approach to be the most favourable, making our system a desirable addition for intraoperative HSI.

* To be presented at MICCAI 2023 
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