A generalisable head MRI defacing pipeline: Evaluation on 2,566 meningioma scans

Reliable MRI defacing techniques to safeguard patient privacy while preserving brain anatomy are critical for research collaboration. Existing methods often struggle with incomplete defacing or degradation of brain tissue regions. We present a robust, generalisable defacing pipeline for high-resolution MRI that integrates atlas-based registration with brain masking. Our method was evaluated on 2,566 heterogeneous clinical scans for meningioma and achieved a 99.92 per cent success rate (2,564/2,566) upon visual inspection. Excellent anatomical preservation is demonstrated with a Dice similarity coefficient of 0.9975 plus or minus 0.0023 between brain masks automatically extracted from the original and defaced volumes. Source code is available at https://github.com/cai4cai/defacing_pipeline.

UltraFlwr -- An Efficient Federated Medical and Surgical Object Detection Framework

Object detection shows promise for medical and surgical applications such as cell counting and tool tracking. However, its faces multiple real-world edge deployment challenges including limited high-quality annotated data, data sharing restrictions, and computational constraints. In this work, we introduce UltraFlwr, a framework for federated medical and surgical object detection. By leveraging Federated Learning (FL), UltraFlwr enables decentralized model training across multiple sites without sharing raw data. To further enhance UltraFlwr's efficiency, we propose YOLO-PA, a set of novel Partial Aggregation (PA) strategies specifically designed for YOLO models in FL. YOLO-PA significantly reduces communication overhead by up to 83% per round while maintaining performance comparable to Full Aggregation (FA) strategies. Our extensive experiments on BCCD and m2cai16-tool-locations datasets demonstrate that YOLO-PA not only provides better client models compared to client-wise centralized training and FA strategies, but also facilitates efficient training and deployment across resource-constrained edge devices. Further, we also establish one of the first benchmarks in federated medical and surgical object detection. This paper advances the feasibility of training and deploying detection models on the edge, making federated object detection more practical for time-critical and resource-constrained medical and surgical applications. UltraFlwr is publicly available at https://github.com/KCL-BMEIS/UltraFlwr.

OOD-SEG: Out-Of-Distribution detection for image SEGmentation with sparse multi-class positive-only annotations

Despite significant advancements, segmentation based on deep neural networks in medical and surgical imaging faces several challenges, two of which we aim to address in this work. First, acquiring complete pixel-level segmentation labels for medical images is time-consuming and requires domain expertise. Second, typical segmentation pipelines cannot detect out-of-distribution (OOD) pixels, leaving them prone to spurious outputs during deployment. In this work, we propose a novel segmentation approach exploiting OOD detection that learns only from sparsely annotated pixels from multiple positive-only classes. %but \emph{no background class} annotation. These multi-class positive annotations naturally fall within the in-distribution (ID) set. Unlabelled pixels may contain positive classes but also negative ones, including what is typically referred to as \emph{background} in standard segmentation formulations. Here, we forgo the need for background annotation and consider these together with any other unseen classes as part of the OOD set. Our framework can integrate, at a pixel-level, any OOD detection approaches designed for classification tasks. To address the lack of existing OOD datasets and established evaluation metric for medical image segmentation, we propose a cross-validation strategy that treats held-out labelled classes as OOD. Extensive experiments on both multi-class hyperspectral and RGB surgical imaging datasets demonstrate the robustness and generalisation capability of our proposed framework.

Scribble-Based Interactive Segmentation of Medical Hyperspectral Images

Hyperspectral imaging (HSI) is an advanced medical imaging modality that captures optical data across a broad spectral range, providing novel insights into the biochemical composition of tissues. HSI may enable precise differentiation between various tissue types and pathologies, making it particularly valuable for tumour detection, tissue classification, and disease diagnosis. Deep learning-based segmentation methods have shown considerable advancements, offering automated and accurate results. However, these methods face challenges with HSI datasets due to limited annotated data and discrepancies from hardware and acquisition techniques~\cite{clancy2020surgical,studier2023heiporspectral}. Variability in clinical protocols also leads to different definitions of structure boundaries. Interactive segmentation methods, utilizing user knowledge and clinical insights, can overcome these issues and achieve precise segmentation results \cite{zhao2013overview}. This work introduces a scribble-based interactive segmentation framework for medical hyperspectral images. The proposed method utilizes deep learning for feature extraction and a geodesic distance map generated from user-provided scribbles to obtain the segmentation results. The experiment results show that utilising the geodesic distance maps based on deep learning-extracted features achieved better segmentation results than geodesic distance maps directly generated from hyperspectral images, reconstructed RGB images, or Euclidean distance maps.

A self-supervised and adversarial approach to hyperspectral demosaicking and RGB reconstruction in surgical imaging

Hyperspectral imaging holds promises in surgical imaging by offering biological tissue differentiation capabilities with detailed information that is invisible to the naked eye. For intra-operative guidance, real-time spectral data capture and display is mandated. Snapshot mosaic hyperspectral cameras are currently seen as the most suitable technology given this requirement. However, snapshot mosaic imaging requires a demosaicking algorithm to fully restore the spatial and spectral details in the images. Modern demosaicking approaches typically rely on synthetic datasets to develop supervised learning methods, as it is practically impossible to simultaneously capture both snapshot and high-resolution spectral images of the exact same surgical scene. In this work, we present a self-supervised demosaicking and RGB reconstruction method that does not depend on paired high-resolution data as ground truth. We leverage unpaired standard high-resolution surgical microscopy images, which only provide RGB data but can be collected during routine surgeries. Adversarial learning complemented by self-supervised approaches are used to drive our hyperspectral-based RGB reconstruction into resembling surgical microscopy images and increasing the spatial resolution of our demosaicking. The spatial and spectral fidelity of the reconstructed hyperspectral images have been evaluated quantitatively. Moreover, a user study was conducted to evaluate the RGB visualisation generated from these spectral images. Both spatial detail and colour accuracy were assessed by neurosurgical experts. Our proposed self-supervised demosaicking method demonstrates improved results compared to existing methods, demonstrating its potential for seamless integration into intra-operative workflows.

Brain Tumor Segmentation (BraTS) Challenge 2024: Meningioma Radiotherapy Planning Automated Segmentation

The 2024 Brain Tumor Segmentation Meningioma Radiotherapy (BraTS-MEN-RT) challenge aims to advance automated segmentation algorithms using the largest known multi-institutional dataset of radiotherapy planning brain MRIs with expert-annotated target labels for patients with intact or post-operative meningioma that underwent either conventional external beam radiotherapy or stereotactic radiosurgery. Each case includes a defaced 3D post-contrast T1-weighted radiotherapy planning MRI in its native acquisition space, accompanied by a single-label "target volume" representing the gross tumor volume (GTV) and any at-risk post-operative site. Target volume annotations adhere to established radiotherapy planning protocols, ensuring consistency across cases and institutions. For pre-operative meningiomas, the target volume encompasses the entire GTV and associated nodular dural tail, while for post-operative cases, it includes at-risk resection cavity margins as determined by the treating institution. Case annotations were reviewed and approved by expert neuroradiologists and radiation oncologists. Participating teams will develop, containerize, and evaluate automated segmentation models using this comprehensive dataset. Model performance will be assessed using the lesion-wise Dice Similarity Coefficient and the 95% Hausdorff distance. The top-performing teams will be recognized at the Medical Image Computing and Computer Assisted Intervention Conference in October 2024. BraTS-MEN-RT is expected to significantly advance automated radiotherapy planning by enabling precise tumor segmentation and facilitating tailored treatment, ultimately improving patient outcomes.

A Clinical Guideline Driven Automated Linear Feature Extraction for Vestibular Schwannoma

Vestibular Schwannoma is a benign brain tumour that grows from one of the balance nerves. Patients may be treated by surgery, radiosurgery or with a conservative "wait-and-scan" strategy. Clinicians typically use manually extracted linear measurements to aid clinical decision making. This work aims to automate and improve this process by using deep learning based segmentation to extract relevant clinical features through computational algorithms. To the best of our knowledge, our study is the first to propose an automated approach to replicate local clinical guidelines. Our deep learning based segmentation provided Dice-scores of 0.8124 +- 0.2343 and 0.8969 +- 0.0521 for extrameatal and whole tumour regions respectively for T2 weighted MRI, whereas 0.8222 +- 0.2108 and 0.9049 +- 0.0646 were obtained for T1 weighted MRI. We propose a novel algorithm to choose and extract the most appropriate maximum linear measurement from the segmented regions based on the size of the extrameatal portion of the tumour. Using this tool, clinicians will be provided with a visual guide and related metrics relating to tumour progression that will function as a clinical decision aid. In this study, we utilize 187 scans obtained from 50 patients referred to a tertiary specialist neurosurgical service in the United Kingdom. The measurements extracted manually by an expert neuroradiologist indicated a significant correlation with the automated measurements (p < 0.0001).

MedShapeNet -- A Large-Scale Dataset of 3D Medical Shapes for Computer Vision

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: https://medshapenet.ikim.nrw/

Synthetic white balancing for intra-operative hyperspectral imaging

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.

Deep Reinforcement Learning Based System for Intraoperative Hyperspectral Video Autofocusing

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.