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We present a new approach for vision-based force estimation in Minimally Invasive Robotic Surgery based on frequency domain basis of motion of organs derived directly from video. Using internal movements generated by natural processes like breathing or the cardiac cycle, we infer the image-space basis of the motion on the frequency domain. As we are working with this representation, we discretize the problem to a limited amount of low-frequencies to build an image-space mechanical model of the environment. We use this pre-built model to define our force estimation problem as a dynamic constraint problem. We demonstrate that this method can estimate point contact forces reliably for silicone phantom and ex-vivo experiments, matching real readings from a force sensor. In addition, we perform qualitative experiments in which we synthesize coherent force textures from surgical videos over a certain region of interest selected by the user. Our method demonstrates good results for both quantitative and qualitative analysis, providing a good starting point for a purely vision-based method for surgical force estimation.

Accurate brain lesion delineation is important for planning neurosurgical treatment. Automatic brain lesion segmentation methods based on convolutional neural networks have demonstrated remarkable performance. However, neural network performance is constrained by the lack of large-scale well-annotated training datasets. In this manuscript, we propose a comprehensive framework to efficiently generate new samples for training a brain lesion segmentation model. We first train a lesion generator, based on an adversarial autoencoder, in a self-supervised manner. Next, we utilize a novel image composition algorithm, Soft Poisson Blending, to seamlessly combine synthetic lesions and brain images to obtain training samples. Finally, to effectively train the brain lesion segmentation model with augmented images we introduce a new prototype consistence regularization to align real and synthetic features. Our framework is validated by extensive experiments on two public brain lesion segmentation datasets: ATLAS v2.0 and Shift MS. Our method outperforms existing brain image data augmentation schemes. For instance, our method improves the Dice from 50.36% to 60.23% compared to the U-Net with conventional data augmentation techniques for the ATLAS v2.0 dataset., Comment: 11 pages, 7 figures, 8 tables

The surgical intervention is crucial to patient healthcare, and many studies have developed advanced algorithms to provide understanding and decision-making assistance for surgeons. Despite great progress, these algorithms are developed for a single specific task and scenario, and in practice require the manual combination of different functions, thus limiting the applicability. Thus, an intelligent and versatile surgical assistant is expected to accurately understand the surgeon's intentions and accordingly conduct the specific tasks to support the surgical process. In this work, by leveraging advanced multimodal large language models (MLLMs), we propose a Versatile Surgery Assistant (VS-Assistant) that can accurately understand the surgeon's intention and complete a series of surgical understanding tasks, e.g., surgical scene analysis, surgical instrument detection, and segmentation on demand. Specifically, to achieve superior surgical multimodal understanding, we devise a mixture of projectors (MOP) module to align the surgical MLLM in VS-Assistant to balance the natural and surgical knowledge. Moreover, we devise a surgical Function-Calling Tuning strategy to enable the VS-Assistant to understand surgical intentions, and thus make a series of surgical function calls on demand to meet the needs of the surgeons. Extensive experiments on neurosurgery data confirm that our VS-Assistant can understand the surgeon's intention more accurately than the existing MLLM, resulting in overwhelming performance in textual analysis and visual tasks. Source code and models will be made public.

Purpose: Autonomous navigation of devices in endovascular interventions can decrease operation times, improve decision-making during surgery, and reduce operator radiation exposure while increasing access to treatment. This systematic review explores recent literature to assess the impact, challenges, and opportunities artificial intelligence (AI) has for the autonomous endovascular intervention navigation. Methods: PubMed and IEEEXplore databases were queried. Eligibility criteria included studies investigating the use of AI in enabling the autonomous navigation of catheters/guidewires in endovascular interventions. Following PRISMA, articles were assessed using QUADAS-2. PROSPERO: CRD42023392259. Results: Among 462 studies, fourteen met inclusion criteria. Reinforcement learning (9/14, 64%) and learning from demonstration (7/14, 50%) were used as data-driven models for autonomous navigation. Studies predominantly utilised physical phantoms (10/14, 71%) and in silico (4/14, 29%) models. Experiments within or around the blood vessels of the heart were reported by the majority of studies (10/14, 71%), while simple non-anatomical vessel platforms were used in three studies (3/14, 21%), and the porcine liver venous system in one study. We observed that risk of bias and poor generalisability were present across studies. No procedures were performed on patients in any of the studies reviewed. Studies lacked patient selection criteria, reference standards, and reproducibility, resulting in low clinical evidence levels. Conclusions: AI's potential in autonomous endovascular navigation is promising, but in an experimental proof-of-concept stage, with a technology readiness level of 3. We highlight that reference standards with well-identified performance metrics are crucial to allow for comparisons of data-driven algorithms proposed in the years to come., Comment: Abstract shortened for arXiv character limit

Artificial neural networks trained on large, expert-labelled datasets are considered state-of-the-art for a range of medical image recognition tasks. However, categorically labelled datasets are time-consuming to generate and constrain classification to a pre-defined, fixed set of classes. For neuroradiological applications in particular, this represents a barrier to clinical adoption. To address these challenges, we present a self-supervised text-vision framework that learns to detect clinically relevant abnormalities in brain MRI scans by directly leveraging the rich information contained in accompanying free-text neuroradiology reports. Our training approach consisted of two-steps. First, a dedicated neuroradiological language model - NeuroBERT - was trained to generate fixed-dimensional vector representations of neuroradiology reports (N = 50,523) via domain-specific self-supervised learning tasks. Next, convolutional neural networks (one per MRI sequence) learnt to map individual brain scans to their corresponding text vector representations by optimising a mean square error loss. Once trained, our text-vision framework can be used to detect abnormalities in unreported brain MRI examinations by scoring scans against suitable query sentences (e.g., 'there is an acute stroke', 'there is hydrocephalus' etc.), enabling a range of classification-based applications including automated triage. Potentially, our framework could also serve as a clinical decision support tool, not only by suggesting findings to radiologists and detecting errors in provisional reports, but also by retrieving and displaying examples of pathologies from historical examinations that could be relevant to the current case based on textual descriptors., Comment: Under Review

In surgical skill assessment, Objective Structured Assessments of Technical Skills (OSATS scores) and the Global Rating Scale (GRS) are established tools for evaluating the performance of surgeons during training. These metrics, coupled with feedback on their performance, enable surgeons to improve and achieve standards of practice. Recent studies on the open-source dataset JIGSAW, which contains both GRS and OSATS labels, have focused on regressing GRS scores from kinematic signals, video data, or a combination of both. In this paper, we argue that regressing the GRS score, a unitless value, by itself is too restrictive, and variations throughout the surgical trial do not hold significant clinical meaning. To address this gap, we developed a recurrent transformer model that outputs the surgeon's performance throughout their training session by relating the model's hidden states to five OSATS scores derived from kinematic signals. These scores are averaged and aggregated to produce a GRS prediction, enabling assessment of the model's performance against the state-of-the-art (SOTA). We report Spearman's Correlation Coefficient (SCC), demonstrating that our model outperforms SOTA models for all tasks, except for Suturing under the leave-one-subject-out (LOSO) scheme (SCC 0.68-0.89), while achieving comparable performance for suturing and across tasks under the leave-one-user-out (LOUO) scheme (SCC 0.45-0.68) and beating SOTA for Needle Passing (0.69). We argue that relating final OSATS scores to short instances throughout a surgeon's procedure is more clinically meaningful than a single GRS score. This approach also allows us to translate quantitative predictions into qualitative feedback, which is crucial for any automated surgical skill assessment pipeline. A senior surgeon validated our model's behaviour and agreed with the semi-supervised predictions 77 \% (p = 0.006) of the time.

Whole brain parcellation requires inferring hundreds of segmentation labels in large image volumes and thus presents significant practical challenges for deep learning approaches. We introduce label merge-and-split, a method that first greatly reduces the effective number of labels required for learning-based whole brain parcellation and then recovers original labels. Using a greedy graph colouring algorithm, our method automatically groups and merges multiple spatially separate labels prior to model training and inference. The merged labels may be semantically unrelated. A deep learning model is trained to predict merged labels. At inference time, original labels are restored using atlas-based influence regions. In our experiments, the proposed approach reduces the number of labels by up to 68% while achieving segmentation accuracy comparable to the baseline method without label merging and splitting. Moreover, model training and inference times as well as GPU memory requirements were reduced significantly. The proposed method can be applied to all semantic segmentation tasks with a large number of spatially separate classes within an atlas-based prior.

Stroke is a leading cause of disability and death. Effective treatment decisions require early and informative vascular imaging. 4D perfusion imaging is ideal but rarely available within the first hour after stroke, whereas plain CT and CTA usually are. Hence, we propose a framework to extract a predicted perfusion map (PPM) derived from CT and CTA images. In all eighteen patients, we found significantly high spatial similarity (with average Spearman's correlation = 0.7893) between our predicted perfusion map (PPM) and the T-max map derived from 4D-CTP. Voxelwise correlations between the PPM and National Institutes of Health Stroke Scale (NIHSS) subscores for L/R hand motor, gaze, and language on a large cohort of 2,110 subjects reliably mapped symptoms to expected infarct locations. Therefore our PPM could serve as an alternative for 4D perfusion imaging, if the latter is unavailable, to investigate blood perfusion in the first hours after hospital admission., Comment: Accepted and presented in SWITCH2023: Stroke Workshop on Imaging and Treatment CHallenges (MICCAI 2023, Vancouver Canada)

Diffusion-weighted MRI (DWI) is essential for stroke diagnosis, treatment decisions, and prognosis. However, image and disease variability hinder the development of generalizable AI algorithms with clinical value. We address this gap by presenting a novel ensemble algorithm derived from the 2022 Ischemic Stroke Lesion Segmentation (ISLES) challenge. ISLES'22 provided 400 patient scans with ischemic stroke from various medical centers, facilitating the development of a wide range of cutting-edge segmentation algorithms by the research community. Through collaboration with leading teams, we combined top-performing algorithms into an ensemble model that overcomes the limitations of individual solutions. Our ensemble model achieved superior ischemic lesion detection and segmentation accuracy on our internal test set compared to individual algorithms. This accuracy generalized well across diverse image and disease variables. Furthermore, the model excelled in extracting clinical biomarkers. Notably, in a Turing-like test, neuroradiologists consistently preferred the algorithm's segmentations over manual expert efforts, highlighting increased comprehensiveness and precision. Validation using a real-world external dataset (N=1686) confirmed the model's generalizability. The algorithm's outputs also demonstrated strong correlations with clinical scores (admission NIHSS and 90-day mRS) on par with or exceeding expert-derived results, underlining its clinical relevance. This study offers two key findings. First, we present an ensemble algorithm (https://github.com/Tabrisrei/ISLES22_Ensemble) that detects and segments ischemic stroke lesions on DWI across diverse scenarios on par with expert (neuro)radiologists. Second, we show the potential for biomedical challenge outputs to extend beyond the challenge's initial objectives, demonstrating their real-world clinical applicability.

Rapid advancements in medical image segmentation performance have been significantly driven by the development of Convolutional Neural Networks (CNNs) and Vision Transformers (ViTs). These models follow the discriminative pixel-wise classification learning paradigm and often have limited ability to generalize across diverse medical imaging datasets. In this manuscript, we introduce Generative Medical Segmentation (GMS), a novel approach leveraging a generative model to perform image segmentation. Concretely, GMS employs a robust pre-trained vision foundation model to extract latent representations for images and corresponding ground truth masks, followed by a model that learns a mapping function from the image to the mask in the latent space. Once trained, the model generates an estimated segmentation mask using the pre-trained vision foundation model to decode the predicted latent representation back into the image space. The design of GMS leads to fewer trainable parameters in the model which reduces the risk of overfitting and enhances its generalization capability. Our experimental analysis across five public datasets in different medical imaging domains demonstrates GMS outperforms existing discriminative and generative segmentation models. Furthermore, GMS is able to generalize well across datasets from different centers within the same imaging modality. Our experiments suggest GMS offers a scalable and effective solution for medical image segmentation. GMS implementation and trained model weights are available at https://github.com/King-HAW/GMS.

Recently, automated medical image segmentation methods based on deep learning have achieved great success. However, they heavily rely on large annotated datasets, which are costly and time-consuming to acquire. Few-shot learning aims to overcome the need for annotated data by using a small labeled dataset, known as a support set, to guide predicting labels for new, unlabeled images, known as the query set. Inspired by this paradigm, we introduce MatchSeg, a novel framework that enhances medical image segmentation through strategic reference image matching. We leverage contrastive language-image pre-training (CLIP) to select highly relevant samples when defining the support set. Additionally, we design a joint attention module to strengthen the interaction between support and query features, facilitating a more effective knowledge transfer between support and query sets. We validated our method across four public datasets. Experimental results demonstrate superior segmentation performance and powerful domain generalization ability of MatchSeg against existing methods for domain-specific and cross-domain segmentation tasks. Our code is made available at https://github.com/keeplearning-again/MatchSeg, Comment: International Conference on Bioinformatics and Biomedicine (BIBM 2024)

This study introduces a novel framework for enhancing domain generalization in medical imaging, specifically focusing on utilizing unlabelled multi-view colour fundus photographs. Unlike traditional approaches that rely on single-view imaging data and face challenges in generalizing across diverse clinical settings, our method leverages the rich information in the unlabelled multi-view imaging data to improve model robustness and accuracy. By incorporating a class balancing method, a test-time adaptation technique and a multi-view optimization strategy, we address the critical issue of domain shift that often hampers the performance of machine learning models in real-world applications. Experiments comparing various state-of-the-art domain generalization and test-time optimization methodologies show that our approach consistently outperforms when combined with existing baseline and state-of-the-art methods. We also show our online method improves all existing techniques. Our framework demonstrates improvements in domain generalization capabilities and offers a practical solution for real-world deployment by facilitating online adaptation to new, unseen datasets. Our code is available at https://github.com/zgy600/RetiGen .

Accurate identification of End-Diastolic (ED) and End-Systolic (ES) frames is key for cardiac function assessment through echocardiography. However, traditional methods face several limitations: they require extensive amounts of data, extensive annotations by medical experts, significant training resources, and often lack robustness. Addressing these challenges, we proposed an unsupervised and training-free method, our novel approach leverages unsupervised segmentation to enhance fault tolerance against segmentation inaccuracies. By identifying anchor points and analyzing directional deformation, we effectively reduce dependence on the accuracy of initial segmentation images and enhance fault tolerance, all while improving robustness. Tested on Echo-dynamic and CAMUS datasets, our method achieves comparable accuracy to learning-based models without their associated drawbacks. The code is available at https://github.com/MRUIL/DDSB

Video-based surgical instrument segmentation plays an important role in robot-assisted surgeries. Unlike supervised settings, unsupervised segmentation relies heavily on motion cues, which are challenging to discern due to the typically lower quality of optical flow in surgical footage compared to natural scenes. This presents a considerable burden for the advancement of unsupervised segmentation techniques. In our work, we address the challenge of enhancing model performance despite the inherent limitations of low-quality optical flow. Our methodology employs a three-pronged approach: extracting boundaries directly from the optical flow, selectively discarding frames with inferior flow quality, and employing a fine-tuning process with variable frame rates. We thoroughly evaluate our strategy on the EndoVis2017 VOS dataset and Endovis2017 Challenge dataset, where our model demonstrates promising results, achieving a mean Intersection-over-Union (mIoU) of 0.75 and 0.72, respectively. Our findings suggest that our approach can greatly decrease the need for manual annotations in clinical environments and may facilitate the annotation process for new datasets. The code is available at https://github.com/wpr1018001/Rethinking-Low-quality-Optical-Flow.git

Intra-operative recognition of surgical phases holds significant potential for enhancing real-time contextual awareness in the operating room. However, we argue that online recognition, while beneficial, primarily lends itself to post-operative video analysis due to its limited direct impact on the actual surgical decisions and actions during ongoing procedures. In contrast, we contend that the prediction and anticipation of surgical phases are inherently more valuable for intra-operative assistance, as they can meaningfully influence a surgeon's immediate and long-term planning by providing foresight into future steps. To address this gap, we propose a dual approach that simultaneously recognises the current surgical phase and predicts upcoming ones, thus offering comprehensive intra-operative assistance and guidance on the expected remaining workflow. Our novel method, Surgical Phase Recognition and Anticipation (SuPRA), leverages past and current information for accurate intra-operative phase recognition while using future segments for phase prediction. This unified approach challenges conventional frameworks that treat these objectives separately. We have validated SuPRA on two reputed datasets, Cholec80 and AutoLaparo21, where it demonstrated state-of-the-art performance with recognition accuracies of 91.8% and 79.3%, respectively. Additionally, we introduce and evaluate our model using new segment-level evaluation metrics, namely Edit and F1 Overlap scores, for a more temporal assessment of segment classification. In conclusion, SuPRA presents a new multi-task approach that paves the way for improved intra-operative assistance through surgical phase recognition and prediction of future events.

Real-time 6 DOF localization of bronchoscopes is crucial for enhancing intervention quality. However, current vision-based technologies struggle to balance between generalization to unseen data and computational speed. In this study, we propose a Depth-based Dual-Loop framework for real-time Visually Navigated Bronchoscopy (DD-VNB) that can generalize across patient cases without the need of re-training. The DD-VNB framework integrates two key modules: depth estimation and dual-loop localization. To address the domain gap among patients, we propose a knowledge-embedded depth estimation network that maps endoscope frames to depth, ensuring generalization by eliminating patient-specific textures. The network embeds view synthesis knowledge into a cycle adversarial architecture for scale-constrained monocular depth estimation. For real-time performance, our localization module embeds a fast ego-motion estimation network into the loop of depth registration. The ego-motion inference network estimates the pose change of the bronchoscope in high frequency while depth registration against the pre-operative 3D model provides absolute pose periodically. Specifically, the relative pose changes are fed into the registration process as the initial guess to boost its accuracy and speed. Experiments on phantom and in-vivo data from patients demonstrate the effectiveness of our framework: 1) monocular depth estimation outperforms SOTA, 2) localization achieves an accuracy of Absolute Tracking Error (ATE) of 4.7 $\pm$ 3.17 mm in phantom and 6.49 $\pm$ 3.88 mm in patient data, 3) with a frame-rate approaching video capture speed, 4) without the necessity of case-wise network retraining. The framework's superior speed and accuracy demonstrate its promising clinical potential for real-time bronchoscopic navigation.

In this study, we address the challenging task of bridging the modality gap between learning from language and inference for visual tasks, including Visual Question Answering (VQA), Image Captioning (IC) and Visual Entailment (VE). We train models for these tasks in a zero-shot cross-modal transfer setting, a domain where the previous state-of-the-art method relied on the fixed scale noise injection, often compromising the semantic content of the original modality embedding. To combat it, we propose a novel method called Adaptive ranged cosine Similarity injected noise (ArcSin). First, we introduce an innovative adaptive noise scale that effectively generates the textual elements with more variability while preserving the original text feature's integrity. Second, a similarity pool strategy is employed, expanding the domain generalization potential by broadening the overall noise scale. This dual strategy effectively widens the scope of the original domain while safeguarding content integrity. Our empirical results demonstrate that these models closely rival those trained on images in terms of performance. Specifically, our method exhibits substantial improvements over the previous state-of-the-art, achieving gains of 1.9 and 1.1 CIDEr points in S-Cap and M-Cap, respectively. Additionally, we observe increases of 1.5 percentage points (pp), 1.4 pp, and 1.4 pp in accuracy for VQA, VQA-E, and VE, respectively, pushing the boundaries of what is achievable within the constraints of image-trained model benchmarks. The code will be released.

Precisely determining the contact force during safe interaction in Minimally Invasive Robotic Surgery (MIRS) is still an open research challenge. Inspired by post-operative qualitative analysis from surgical videos, the use of cross-modality data driven deep neural network models has been one of the newest approaches to predict sensorless force trends. However, these methods required for large and variable datasets which are not currently available. In this paper, we present a new vision-haptic dataset (DaFoEs) with variable soft environments for the training of deep neural models. In order to reduce the bias from a single dataset, we present a pipeline to generalize different vision and state data inputs for mixed dataset training, using a previously validated dataset with different setup. Finally, we present a variable encoder-decoder architecture to predict the forces done by the laparoscopic tool using single input or sequence of inputs. For input sequence, we use a recurrent decoder, named with the prefix R, and a new temporal sampling to represent the acceleration of the tool. During our training, we demonstrate that single dataset training tends to overfit to the training data domain, but has difficulties on translating the results across new domains. However, dataset mixing presents a good translation with a mean relative estimated force error of 5% and 12% for the recurrent and non-recurrent models respectively. Our method, also marginally increase the effectiveness of transformers for force estimation up to a maximum of ~15%, as the volume of available data is increase by 150%. In conclusion, we demonstrate that mixing experimental set ups for vision-state force estimation in MIRS is a possible approach towards the general solution of the problem.

Surgical tool segmentation and action recognition are fundamental building blocks in many computer-assisted intervention applications, ranging from surgical skills assessment to decision support systems. Nowadays, learning-based action recognition and segmentation approaches outperform classical methods, relying, however, on large, annotated datasets. Furthermore, action recognition and tool segmentation algorithms are often trained and make predictions in isolation from each other, without exploiting potential cross-task relationships. With the EndoVis 2022 SAR-RARP50 challenge, we release the first multimodal, publicly available, in-vivo, dataset for surgical action recognition and semantic instrumentation segmentation, containing 50 suturing video segments of Robotic Assisted Radical Prostatectomy (RARP). The aim of the challenge is twofold. First, to enable researchers to leverage the scale of the provided dataset and develop robust and highly accurate single-task action recognition and tool segmentation approaches in the surgical domain. Second, to further explore the potential of multitask-based learning approaches and determine their comparative advantage against their single-task counterparts. A total of 12 teams participated in the challenge, contributing 7 action recognition methods, 9 instrument segmentation techniques, and 4 multitask approaches that integrated both action recognition and instrument segmentation. The complete SAR-RARP50 dataset is available at: https://rdr.ucl.ac.uk/projects/SARRARP50_Segmentation_of_surgical_instrumentation_and_Action_Recognition_on_Robot-Assisted_Radical_Prostatectomy_Challenge/191091

The integration of AI into radiology introduces opportunities for improved clinical care provision and efficiency but it demands a meticulous approach to mitigate potential risks as with any other new technology. Beginning with rigorous pre-deployment evaluation and validation, the focus should be on ensuring models meet the highest standards of safety, effectiveness and efficacy for their intended applications. Input and output guardrails implemented during production usage act as an additional layer of protection, identifying and addressing individual failures as they occur. Continuous post-deployment monitoring allows for tracking population-level performance (data drift), fairness, and value delivery over time. Scheduling reviews of post-deployment model performance and educating radiologists about new algorithmic-driven findings is critical for AI to be effective in clinical practice. Recognizing that no single AI solution can provide absolute assurance even when limited to its intended use, the synergistic application of quality assurance at multiple levels - regulatory, clinical, technical, and ethical - is emphasized. Collaborative efforts between stakeholders spanning healthcare systems, industry, academia, and government are imperative to address the multifaceted challenges involved. Trust in AI is an earned privilege, contingent on a broad set of goals, among them transparently demonstrating that the AI adheres to the same rigorous safety, effectiveness and efficacy standards as other established medical technologies. By doing so, developers can instil confidence among providers and patients alike, enabling the responsible scaling of AI and the realization of its potential benefits. The roadmap presented herein aims to expedite the achievement of deployable, reliable, and safe AI in radiology., Comment: 14 pages, 3 figures

The LBR-Stack is a collection of packages that simplify the usage and extend the capabilities of KUKA's Fast Robot Interface (FRI). It is designed for mission critical hard real-time applications. Supported are the KUKA LBR Med 7/14 and KUKA LBR IIWA 7/14 robots in the Gazebo simulation and for communication with real hardware., Comment: Under review at Journal of Open Source Software (JOSS)

Healthcare data is often split into medium/small-sized collections across multiple hospitals and access to it is encumbered by privacy regulations. This brings difficulties to use them for the development of machine learning and deep learning models, which are known to be data-hungry. One way to overcome this limitation is to use collaborative learning (CL) methods, which allow hospitals to work collaboratively to solve a task, without the need to explicitly share local data. In this paper, we address a prostate segmentation problem from MRI in a collaborative scenario by comparing two different approaches: federated learning (FL) and consensus-based methods (CBM). To the best of our knowledge, this is the first work in which CBM, such as label fusion techniques, are used to solve a problem of collaborative learning. In this setting, CBM combine predictions from locally trained models to obtain a federated strong learner with ideally improved robustness and predictive variance properties. Our experiments show that, in the considered practical scenario, CBMs provide equal or better results than FL, while being highly cost-effective. Our results demonstrate that the consensus paradigm may represent a valid alternative to FL for typical training tasks in medical imaging.

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., Comment: 12 pages, 6 figures, to be published on IEEE TMI

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{https://github.com/ReubenDo/MHVAE}., Comment: Accepted at MICCAI 2023

Fetal Magnetic Resonance Imaging at low field strengths is emerging as an exciting direction in perinatal health. Clinical low field (0.55T) scanners are beneficial for fetal imaging due to their reduced susceptibility-induced artefacts, increased T2* values, and wider bore (widening access for the increasingly obese pregnant population). However, the lack of standard automated image processing tools such as segmentation and reconstruction hampers wider clinical use. In this study, we introduce a semi-automatic pipeline using quantitative MRI for the fetal body at low field strength resulting in fast and detailed quantitative T2* relaxometry analysis of all major fetal body organs. Multi-echo dynamic sequences of the fetal body were acquired and reconstructed into a single high-resolution volume using deformable slice-to-volume reconstruction, generating both structural and quantitative T2* 3D volumes. A neural network trained using a semi-supervised approach was created to automatically segment these fetal body 3D volumes into ten different organs (resulting in dice values > 0.74 for 8 out of 10 organs). The T2* values revealed a strong relationship with GA in the lungs, liver, and kidney parenchyma (R^2>0.5). This pipeline was used successfully for a wide range of GAs (17-40 weeks), and is robust to motion artefacts. Low field fetal MRI can be used to perform advanced MRI analysis, and is a viable option for clinical scanning., Comment: Accepted by MICCAI 2023

Recent advances in generative AI have brought incredible breakthroughs in several areas, including medical imaging. These generative models have tremendous potential not only to help safely share medical data via synthetic datasets but also to perform an array of diverse applications, such as anomaly detection, image-to-image translation, denoising, and MRI reconstruction. However, due to the complexity of these models, their implementation and reproducibility can be difficult. This complexity can hinder progress, act as a use barrier, and dissuade the comparison of new methods with existing works. In this study, we present MONAI Generative Models, a freely available open-source platform that allows researchers and developers to easily train, evaluate, and deploy generative models and related applications. Our platform reproduces state-of-art studies in a standardised way involving different architectures (such as diffusion models, autoregressive transformers, and GANs), and provides pre-trained models for the community. We have implemented these models in a generalisable fashion, illustrating that their results can be extended to 2D or 3D scenarios, including medical images with different modalities (like CT, MRI, and X-Ray data) and from different anatomical areas. Finally, we adopt a modular and extensible approach, ensuring long-term maintainability and the extension of current applications for future features.

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., Comment: Early accepted at MICCAI 2023

Methods for out-of-distribution (OOD) detection that scale to 3D data are crucial components of any real-world clinical deep learning system. Classic denoising diffusion probabilistic models (DDPMs) have been recently proposed as a robust way to perform reconstruction-based OOD detection on 2D datasets, but do not trivially scale to 3D data. In this work, we propose to use Latent Diffusion Models (LDMs), which enable the scaling of DDPMs to high-resolution 3D medical data. We validate the proposed approach on near- and far-OOD datasets and compare it to a recently proposed, 3D-enabled approach using Latent Transformer Models (LTMs). Not only does the proposed LDM-based approach achieve statistically significant better performance, it also shows less sensitivity to the underlying latent representation, more favourable memory scaling, and produces better spatial anomaly maps. Code is available at https://github.com/marksgraham/ddpm-ood, Comment: Accepted at MICCAI 2023

Accurately segmenting brain lesions in MRI scans is critical for providing patients with prognoses and neurological monitoring. However, the performance of CNN-based segmentation methods is constrained by the limited training set size. Advanced data augmentation is an effective strategy to improve the model's robustness. However, they often introduce intensity disparities between foreground and background areas and boundary artifacts, which weakens the effectiveness of such strategies. In this paper, we propose a foreground harmonization framework (ARHNet) to tackle intensity disparities and make synthetic images look more realistic. In particular, we propose an Adaptive Region Harmonization (ARH) module to dynamically align foreground feature maps to the background with an attention mechanism. We demonstrate the efficacy of our method in improving the segmentation performance using real and synthetic images. Experimental results on the ATLAS 2.0 dataset show that ARHNet outperforms other methods for image harmonization tasks, and boosts the down-stream segmentation performance. Our code is publicly available at https://github.com/King-HAW/ARHNet., Comment: 9 pages, 4 figures, 3 tables

Automatic segmentation of medical images is a key step for diagnostic and interventional tasks. However, achieving this requires large amounts of annotated volumes, which can be tedious and time-consuming task for expert annotators. In this paper, we introduce DeepEdit, a deep learning-based method for volumetric medical image annotation, that allows automatic and semi-automatic segmentation, and click-based refinement. DeepEdit combines the power of two methods: a non-interactive (i.e. automatic segmentation using nnU-Net, UNET or UNETR) and an interactive segmentation method (i.e. DeepGrow), into a single deep learning model. It allows easy integration of uncertainty-based ranking strategies (i.e. aleatoric and epistemic uncertainty computation) and active learning. We propose and implement a method for training DeepEdit by using standard training combined with user interaction simulation. Once trained, DeepEdit allows clinicians to quickly segment their datasets by using the algorithm in auto segmentation mode or by providing clicks via a user interface (i.e. 3D Slicer, OHIF). We show the value of DeepEdit through evaluation on the PROSTATEx dataset for prostate/prostatic lesions and the Multi-Atlas Labeling Beyond the Cranial Vault (BTCV) dataset for abdominal CT segmentation, using state-of-the-art network architectures as baseline for comparison. DeepEdit could reduce the time and effort annotating 3D medical images compared to DeepGrow alone. Source code is available at https://github.com/Project-MONAI/MONAILabel

Online surgical phase recognition plays a significant role towards building contextual tools that could quantify performance and oversee the execution of surgical workflows. Current approaches are limited since they train spatial feature extractors using frame-level supervision that could lead to incorrect predictions due to similar frames appearing at different phases, and poorly fuse local and global features due to computational constraints which can affect the analysis of long videos commonly encountered in surgical interventions. In this paper, we present a two-stage method, called Long Video Transformer (LoViT) for fusing short- and long-term temporal information that combines a temporally-rich spatial feature extractor and a multi-scale temporal aggregator consisting of two cascaded L-Trans modules based on self-attention, followed by a G-Informer module based on ProbSparse self-attention for processing global temporal information. The multi-scale temporal head then combines local and global features and classifies surgical phases using phase transition-aware supervision. Our approach outperforms state-of-the-art methods on the Cholec80 and AutoLaparo datasets consistently. Compared to Trans-SVNet, LoViT achieves a 2.4 pp (percentage point) improvement in video-level accuracy on Cholec80 and a 3.1 pp improvement on AutoLaparo. Moreover, it achieves a 5.3 pp improvement in phase-level Jaccard on AutoLaparo and a 1.55 pp improvement on Cholec80. Our results demonstrate the effectiveness of our approach in achieving state-of-the-art performance of surgical phase recognition on two datasets of different surgical procedures and temporal sequencing characteristics whilst introducing mechanisms that cope with long videos., Comment: Code link: https://github.com/MRUIL/LoViT

Cancer is a highly heterogeneous condition that can occur almost anywhere in the human body. 18F-fluorodeoxyglucose is an imaging modality commonly used to detect cancer due to its high sensitivity and clear visualisation of the pattern of metabolic activity. Nonetheless, as cancer is highly heterogeneous, it is challenging to train general-purpose discriminative cancer detection models, with data availability and disease complexity often cited as a limiting factor. Unsupervised anomaly detection models have been suggested as a putative solution. These models learn a healthy representation of tissue and detect cancer by predicting deviations from the healthy norm, which requires models capable of accurately learning long-range interactions between organs and their imaging patterns with high levels of expressivity. Such characteristics are suitably satisfied by transformers, which have been shown to generate state-of-the-art results in unsupervised anomaly detection by training on normal data. This work expands upon such approaches by introducing multi-modal conditioning of the transformer via cross-attention i.e. supplying anatomical reference from paired CT. Using 294 whole-body PET/CT samples, we show that our anomaly detection method is robust and capable of achieving accurate cancer localization results even in cases where normal training data is unavailable. In addition, we show the efficacy of this approach on out-of-sample data showcasing the generalizability of this approach with limited training data. Lastly, we propose to combine model uncertainty with a new kernel density estimation approach, and show that it provides clinically and statistically significant improvements when compared to the classic residual-based anomaly maps. Overall, a superior performance is demonstrated against leading state-of-the-art alternatives, drawing attention to the potential of these approaches., Comment: Accepted for publication at the Journal of Machine Learning for Biomedical Imaging (MELBA) https://melba-journal.org/2023:006

Visual discrimination of clinical tissue types remains challenging, with traditional RGB imaging providing limited contrast for such tasks. Hyperspectral imaging (HSI) is a promising technology providing rich spectral information that can extend far beyond three-channel RGB imaging. Moreover, recently developed snapshot HSI cameras enable real-time imaging with significant potential for clinical applications. Despite this, the investigation into the relative performance of HSI over RGB imaging for semantic segmentation purposes has been limited, particularly in the context of medical imaging. Here we compare the performance of state-of-the-art deep learning image segmentation methods when trained on hyperspectral images, RGB images, hyperspectral pixels (minus spatial context), and RGB pixels (disregarding spatial context). To achieve this, we employ the recently released Oral and Dental Spectral Image Database (ODSI-DB), which consists of 215 manually segmented dental reflectance spectral images with 35 different classes across 30 human subjects. The recent development of snapshot HSI cameras has made real-time clinical HSI a distinct possibility, though successful application requires a comprehensive understanding of the additional information HSI offers. Our work highlights the relative importance of spectral resolution, spectral range, and spatial information to both guide the development of HSI cameras and inform future clinical HSI applications.

The performance of deep learning (DL) algorithms is heavily influenced by the quantity and the quality of the annotated data. However, in Surgical Data Science, access to it is limited. It is thus unsurprising that substantial research efforts are made to develop methods aiming at mitigating the scarcity of annotated SDS data. In parallel, an increasing number of Computer Assisted Interventions (CAI) datasets are being released, although the scale of these remain limited. On these premises, data curation is becoming a key element of many SDS research endeavors. Surgical video datasets are demanding to curate and would benefit from dedicated support tools. In this work, we propose to summarize surgical videos into storyboards or collages of representative frames to ease visualization, annotation, and processing. Video summarization is well-established for natural images. However, state-of-the-art methods typically rely on models trained on human-made annotations, few methods have been evaluated on surgical videos, and the availability of software packages for the task is limited. We present videosum, an easy-to-use and open-source Python library to generate storyboards from surgical videos that contains a variety of unsupervised methods., Comment: Camera-ready version accepted at CRAS 2023

The gold standard in the treatment of ischaemic stroke is set by evidence from randomized controlled trials. Yet the manifest complexity of the brain's functional, connective, and vascular architectures introduces heterogeneity in treatment susceptibility that violates the underlying statistical premisses, potentially leading to substantial errors at both individual and population levels. The counterfactual nature of therapeutic inference has made quantifying the impact of this defect difficult. Combining large-scale meta-analytic connective, functional, genetic expression, and receptor distribution data with high-resolution maps of 4 119 acute ischaemic lesions, here we conduct a comprehensive series of semi-synthetic virtual interventional trials, quantifying the fidelity of the traditional approach in inferring individual treatment effects against biologically plausible, empirically informed ground truths, across 103 628 800 distinct simulations. Combining deep generative models expressive enough to capture the observed lesion heterogeneity with flexible causal modelling, we find that the richness of the lesion representation is decisive in determining individual-level fidelity, even where freedom from treatment allocation bias cannot be guaranteed. Our results indicate that complex modelling with richly represented lesion data is critical to individualized prescriptive inference in ischaemic stroke., Comment: 131 pages

Artificial Intelligence (AI) has become commonplace to solve routine everyday tasks. Because of the exponential growth in medical imaging data volume and complexity, the workload on radiologists is steadily increasing. We project that the gap between the number of imaging exams and the number of expert radiologist readers required to cover this increase will continue to expand, consequently introducing a demand for AI-based tools that improve the efficiency with which radiologists can comfortably interpret these exams. AI has been shown to improve efficiency in medical-image generation, processing, and interpretation, and a variety of such AI models have been developed across research labs worldwide. However, very few of these, if any, find their way into routine clinical use, a discrepancy that reflects the divide between AI research and successful AI translation. To address the barrier to clinical deployment, we have formed MONAI Consortium, an open-source community which is building standards for AI deployment in healthcare institutions, and developing tools and infrastructure to facilitate their implementation. This report represents several years of weekly discussions and hands-on problem solving experience by groups of industry experts and clinicians in the MONAI Consortium. We identify barriers between AI-model development in research labs and subsequent clinical deployment and propose solutions. Our report provides guidance on processes which take an imaging AI model from development to clinical implementation in a healthcare institution. We discuss various AI integration points in a clinical Radiology workflow. We also present a taxonomy of Radiology AI use-cases. Through this report, we intend to educate the stakeholders in healthcare and AI (AI researchers, radiologists, imaging informaticists, and regulators) about cross-disciplinary challenges and possible solutions., Comment: 21 pages; 5 figures

Out-of-distribution detection is crucial to the safe deployment of machine learning systems. Currently, unsupervised out-of-distribution detection is dominated by generative-based approaches that make use of estimates of the likelihood or other measurements from a generative model. Reconstruction-based methods offer an alternative approach, in which a measure of reconstruction error is used to determine if a sample is out-of-distribution. However, reconstruction-based approaches are less favoured, as they require careful tuning of the model's information bottleneck - such as the size of the latent dimension - to produce good results. In this work, we exploit the view of denoising diffusion probabilistic models (DDPM) as denoising autoencoders where the bottleneck is controlled externally, by means of the amount of noise applied. We propose to use DDPMs to reconstruct an input that has been noised to a range of noise levels, and use the resulting multi-dimensional reconstruction error to classify out-of-distribution inputs. We validate our approach both on standard computer-vision datasets and on higher dimension medical datasets. Our approach outperforms not only reconstruction-based methods, but also state-of-the-art generative-based approaches. Code is available at https://github.com/marksgraham/ddpm-ood.

Accurate stroke lesion segmentation plays a pivotal role in stroke rehabilitation research, to provide lesion shape and size information which can be used for quantification of the extent of the stroke and to assess treatment efficacy. Recently, automatic segmentation algorithms using deep learning techniques have been developed and achieved promising results. In this report, we present our stroke lesion segmentation model based on nnU-Net framework, and apply it to the Anatomical Tracings of Lesions After Stroke (ATLAS v2.0) dataset. Furthermore, we describe an effective post-processing strategy that can improve some segmentation metrics. Our method took the first place in the 2022 MICCAI ATLAS Challenge with an average Dice score of 0.6667, Lesion-wise F1 score of 0.5643, Simple Lesion Count score of 4.5367, and Volume Difference score of 8804.9102. Our code and trained model weights are publicly available at https://github.com/King-HAW/ATLAS-R2-Docker-Submission., Comment: Challenge Report, 1st place in 2022 MICCAI ATLAS Challenge

Artificial Intelligence (AI) is having a tremendous impact across most areas of science. Applications of AI in healthcare have the potential to improve our ability to detect, diagnose, prognose, and intervene on human disease. For AI models to be used clinically, they need to be made safe, reproducible and robust, and the underlying software framework must be aware of the particularities (e.g. geometry, physiology, physics) of medical data being processed. This work introduces MONAI, a freely available, community-supported, and consortium-led PyTorch-based framework for deep learning in healthcare. MONAI extends PyTorch to support medical data, with a particular focus on imaging, and provide purpose-specific AI model architectures, transformations and utilities that streamline the development and deployment of medical AI models. MONAI follows best practices for software-development, providing an easy-to-use, robust, well-documented, and well-tested software framework. MONAI preserves the simple, additive, and compositional approach of its underlying PyTorch libraries. MONAI is being used by and receiving contributions from research, clinical and industrial teams from around the world, who are pursuing applications spanning nearly every aspect of healthcare., Comment: www.monai.io

Fetal growth restriction (FGR) is a prevalent pregnancy condition characterised by failure of the fetus to reach its genetically predetermined growth potential. We explore the application of model fitting techniques, linear regression machine learning models, deep learning regression, and Haralick textured features from multi-contrast MRI for multi-fetal organ analysis of FGR. We employed T2 relaxometry and diffusion-weighted MRI datasets (using a combined T2-diffusion scan) for 12 normally grown and 12 FGR gestational age (GA) matched pregnancies. We applied the Intravoxel Incoherent Motion Model and novel multi-compartment models for MRI fetal analysis, which exhibit potential to provide a multi-organ FGR assessment, overcoming the limitations of empirical indicators - such as abnormal artery Doppler findings - to evaluate placental dysfunction. The placenta and fetal liver presented key differentiators between FGR and normal controls (decreased perfusion, abnormal fetal blood motion and reduced fetal blood oxygenation. This may be associated with the preferential shunting of the fetal blood towards the fetal brain. These features were further explored to determine their role in assessing FGR severity, by employing simple machine learning models to predict FGR diagnosis (100\% accuracy in test data, n=5), GA at delivery, time from MRI scan to delivery, and baby weight. Moreover, we explored the use of deep learning to regress the latter three variables. Image texture analysis of the fetal organs demonstrated prominent textural variations in the placental perfusion fractions maps between the groups (p$<$0.0009), and spatial differences in the incoherent fetal capillary blood motion in the liver (p$<$0.009). This research serves as a proof-of-concept, investigating the effect of FGR on fetal organs.

Endoscopic content area refers to the informative area enclosed by the dark, non-informative, border regions present in most endoscopic footage. The estimation of the content area is a common task in endoscopic image processing and computer vision pipelines. Despite the apparent simplicity of the problem, several factors make reliable real-time estimation surprisingly challenging. The lack of rigorous investigation into the topic combined with the lack of a common benchmark dataset for this task has been a long-lasting issue in the field. In this paper, we propose two variants of a lean GPU-based computational pipeline combining edge detection and circle fitting. The two variants differ by relying on handcrafted features, and learned features respectively to extract content area edge point candidates. We also present a first-of-its-kind dataset of manually annotated and pseudo-labelled content areas across a range of surgical indications. To encourage further developments, the curated dataset, and an implementation of both algorithms, has been made public (https://doi.org/10.7303/syn32148000, https://github.com/charliebudd/torch-content-area). We compare our proposed algorithm with a state-of-the-art U-Net-based approach and demonstrate significant improvement in terms of both accuracy (Hausdorff distance: 6.3 px versus 118.1 px) and computational time (Average runtime per frame: 0.13 ms versus 11.2 ms)., Comment: Presented at AE-CAI MICCAI workshop

Deep neural networks have brought remarkable breakthroughs in medical image analysis. However, due to their data-hungry nature, the modest dataset sizes in medical imaging projects might be hindering their full potential. Generating synthetic data provides a promising alternative, allowing to complement training datasets and conducting medical image research at a larger scale. Diffusion models recently have caught the attention of the computer vision community by producing photorealistic synthetic images. In this study, we explore using Latent Diffusion Models to generate synthetic images from high-resolution 3D brain images. We used T1w MRI images from the UK Biobank dataset (N=31,740) to train our models to learn about the probabilistic distribution of brain images, conditioned on covariables, such as age, sex, and brain structure volumes. We found that our models created realistic data, and we could use the conditioning variables to control the data generation effectively. Besides that, we created a synthetic dataset with 100,000 brain images and made it openly available to the scientific community., Comment: 10 pages, 3 figures, Accepted in the Deep Generative Models workshop @ MICCAI 2022

Human anatomy, morphology, and associated diseases can be studied using medical imaging data. However, access to medical imaging data is restricted by governance and privacy concerns, data ownership, and the cost of acquisition, thus limiting our ability to understand the human body. A possible solution to this issue is the creation of a model able to learn and then generate synthetic images of the human body conditioned on specific characteristics of relevance (e.g., age, sex, and disease status). Deep generative models, in the form of neural networks, have been recently used to create synthetic 2D images of natural scenes. Still, the ability to produce high-resolution 3D volumetric imaging data with correct anatomical morphology has been hampered by data scarcity and algorithmic and computational limitations. This work proposes a generative model that can be scaled to produce anatomically correct, high-resolution, and realistic images of the human brain, with the necessary quality to allow further downstream analyses. The ability to generate a potentially unlimited amount of data not only enables large-scale studies of human anatomy and pathology without jeopardizing patient privacy, but also significantly advances research in the field of anomaly detection, modality synthesis, learning under limited data, and fair and ethical AI. Code and trained models are available at: https://github.com/AmigoLab/SynthAnatomy., Comment: 13 pages, 3 figures, 2 tables, accepted at SASHIMI MICCAI 2022

Inter-patient abdominal registration has various applications, from pharmakinematic studies to anatomy modeling. Yet, it remains a challenging application due to the morphological heterogeneity and variability of the human abdomen. Among the various registration methods proposed for this task, probabilistic displacement registration models estimate displacement distribution for a subset of points by comparing feature vectors of points from the two images. These probabilistic models are informative and robust while allowing large displacements by design. As the displacement distributions are typically estimated on a subset of points (which we refer to as driving points), due to computational requirements, we propose in this work to learn a driving points predictor. Compared to previously proposed methods, the driving points predictor is optimized in an end-to-end fashion to infer driving points tailored for a specific registration pipeline. We evaluate the impact of our contribution on two different datasets corresponding to different modalities. Specifically, we compared the performances of 6 different probabilistic displacement registration models when using a driving points predictor or one of 2 other standard driving points selection methods. The proposed method improved performances in 11 out of 12 experiments.

Laser interstitial thermal therapy (LITT) is a novel minimally invasive treatment that is used to ablate intracranial structures to treat mesial temporal lobe epilepsy (MTLE). Region of interest (ROI) segmentation before and after LITT would enable automated lesion quantification to objectively assess treatment efficacy. Deep learning techniques, such as convolutional neural networks (CNNs) are state-of-the-art solutions for ROI segmentation, but require large amounts of annotated data during the training. However, collecting large datasets from emerging treatments such as LITT is impractical. In this paper, we propose a progressive brain lesion synthesis framework (PAVAE) to expand both the quantity and diversity of the training dataset. Concretely, our framework consists of two sequential networks: a mask synthesis network and a mask-guided lesion synthesis network. To better employ extrinsic information to provide additional supervision during network training, we design a condition embedding block (CEB) and a mask embedding block (MEB) to encode inherent conditions of masks to the feature space. Finally, a segmentation network is trained using raw and synthetic lesion images to evaluate the effectiveness of the proposed framework. Experimental results show that our method can achieve realistic synthetic results and boost the performance of down-stream segmentation tasks above traditional data augmentation techniques., Comment: 11 pages, 4 figures, accepted by International Workshop on Simulation and Synthesis in Medical Imaging (SASHIMI 2022)

Data used in image segmentation are not always defined on the same grid. This is particularly true for medical images, where the resolution, field-of-view and orientation can differ across channels and subjects. Images and labels are therefore commonly resampled onto the same grid, as a pre-processing step. However, the resampling operation introduces partial volume effects and blurring, thereby changing the effective resolution and reducing the contrast between structures. In this paper we propose a splat layer, which automatically handles resolution mismatches in the input data. This layer pushes each image onto a mean space where the forward pass is performed. As the splat operator is the adjoint to the resampling operator, the mean-space prediction can be pulled back to the native label space, where the loss function is computed. Thus, the need for explicit resolution adjustment using interpolation is removed. We show on two publicly available datasets, with simulated and real multi-modal magnetic resonance images, that this model improves segmentation results compared to resampling as a pre-processing step., Comment: Accepted for MIUA 2022