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.

Vision and Contact based Optimal Control for Autonomous Trocar Docking

Future operating theatres will be equipped with robots to perform various surgical tasks including, for example, endoscope control. Human-in-the-loop supervisory control architectures where the surgeon selects from several autonomous sequences is already being successfully applied in preclinical tests. Inserting an endoscope into a trocar or introducer is a key step for every keyhole surgical procedure -- hereafter we will only refer to this device as a "trocar". Our goal is to develop a controller for autonomous trocar docking. Autonomous trocar docking is a version of the peg-in-hole problem. Extensive work in the robotics literature addresses this problem. The peg-in-hole problem has been widely studied in the context of assembly where, typically, the hole is considered static and rigid to interaction. In our case, however, the trocar is not fixed and responds to interaction. We consider a variety of surgical procedures where surgeons will utilize contact between the endoscope and trocar in order to complete the insertion successfully. To the best of our knowledge, we have not found literature that explores this particular generalization of the problem directly. Our primary contribution in this work is an optimal control formulation for automated trocar docking. We use a nonlinear optimization program to model the task, minimizing a cost function subject to constraints to find optimal joint configurations. The controller incorporates a geometric model for insertion and a force-feedback (FF) term to ensure patient safety by preventing excessive interaction forces with the trocar. Experiments, demonstrated on a real hardware lab setup, validate the approach. Our method successfully achieves trocar insertion on our real robot lab setup, and simulation trials demonstrate its ability to reduce interaction forces.

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.

Nonrigid Reconstruction of Freehand Ultrasound without a Tracker

Reconstructing 2D freehand Ultrasound (US) frames into 3D space without using a tracker has recently seen advances with deep learning. Predicting good frame-to-frame rigid transformations is often accepted as the learning objective, especially when the ground-truth labels from spatial tracking devices are inherently rigid transformations. Motivated by a) the observed nonrigid deformation due to soft tissue motion during scanning, and b) the highly sensitive prediction of rigid transformation, this study investigates the methods and their benefits in predicting nonrigid transformations for reconstructing 3D US. We propose a novel co-optimisation algorithm for simultaneously estimating rigid transformations among US frames, supervised by ground-truth from a tracker, and a nonrigid deformation, optimised by a regularised registration network. We show that these two objectives can be either optimised using meta-learning or combined by weighting. A fast scattered data interpolation is also developed for enabling frequent reconstruction and registration of non-parallel US frames, during training. With a new data set containing over 357,000 frames in 720 scans, acquired from 60 subjects, the experiments demonstrate that, due to an expanded thus easier-to-optimise solution space, the generalisation is improved with the added deformation estimation, with respect to the rigid ground-truth. The global pixel reconstruction error (assessing accumulative prediction) is lowered from 18.48 to 16.51 mm, compared with baseline rigid-transformation-predicting methods. Using manually identified landmarks, the proposed co-optimisation also shows potentials in compensating nonrigid tissue motion at inference, which is not measurable by tracker-provided ground-truth. The code and data used in this paper are made publicly available at https://github.com/QiLi111/NR-Rec-FUS.

CholecInstanceSeg: A Tool Instance Segmentation Dataset for Laparoscopic Surgery

In laparoscopic and robotic surgery, precise tool instance segmentation is an essential technology for advanced computer-assisted interventions. Although publicly available procedures of routine surgeries exist, they often lack comprehensive annotations for tool instance segmentation. Additionally, the majority of standard datasets for tool segmentation are derived from porcine(pig) surgeries. To address this gap, we introduce CholecInstanceSeg, the largest open-access tool instance segmentation dataset to date. Derived from the existing CholecT50 and Cholec80 datasets, CholecInstanceSeg provides novel annotations for laparoscopic cholecystectomy procedures in patients. Our dataset comprises 41.9k annotated frames extracted from 85 clinical procedures and 64.4k tool instances, each labelled with semantic masks and instance IDs. To ensure the reliability of our annotations, we perform extensive quality control, conduct label agreement statistics, and benchmark the segmentation results with various instance segmentation baselines. CholecInstanceSeg aims to advance the field by offering a comprehensive and high-quality open-access dataset for the development and evaluation of tool instance segmentation algorithms.

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.

An unsupervised learning-based shear wave tracking method for ultrasound elastography

Shear wave elastography involves applying a non-invasive acoustic radiation force to the tissue and imaging the induced deformation to infer its mechanical properties. This work investigates the use of convolutional neural networks to improve displacement estimation accuracy in shear wave imaging. Our training approach is completely unsupervised, which allows to learn the estimation of the induced micro-scale deformations without ground truth labels. We also present an ultrasound simulation dataset where the shear wave propagation has been simulated via finite element method. Our dataset is made publicly available along with this paper, and consists in 150 shear wave propagation simulations in both homogenous and hetegeneous media, which represents a total of 20,000 ultrasound images. We assessed the ability of our learning-based approach to characterise tissue elastic properties (i.e., Young's modulus) on our dataset and compared our results with a classical normalised cross-correlation approach.

Label merge-and-split: A graph-colouring approach for memory-efficient brain parcellation

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.

Average Calibration Error: A Differentiable Loss for Improved Reliability in Image Segmentation

Deep neural networks for medical image segmentation often produce overconfident results misaligned with empirical observations. Such miscalibration, challenges their clinical translation. We propose to use marginal L1 average calibration error (mL1-ACE) as a novel auxiliary loss function to improve pixel-wise calibration without compromising segmentation quality. We show that this loss, despite using hard binning, is directly differentiable, bypassing the need for approximate but differentiable surrogate or soft binning approaches. Our work also introduces the concept of dataset reliability histograms which generalises standard reliability diagrams for refined visual assessment of calibration in semantic segmentation aggregated at the dataset level. Using mL1-ACE, we reduce average and maximum calibration error by 45% and 55% respectively, maintaining a Dice score of 87% on the BraTS 2021 dataset. We share our code here: https://github.com/cai4cai/ACE-DLIRIS