Laparoscopic Scene Analysis for Intraoperative Visualisation of Gamma Probe Signals in Minimally Invasive Cancer Surgery

Cancer remains a significant health challenge worldwide, with a new diagnosis occurring every two minutes in the UK. Surgery is one of the main treatment options for cancer. However, surgeons rely on the sense of touch and naked eye with limited use of pre-operative image data to directly guide the excision of cancerous tissues and metastases due to the lack of reliable intraoperative visualisation tools. This leads to increased costs and harm to the patient where the cancer is removed with positive margins, or where other critical structures are unintentionally impacted. There is therefore a pressing need for more reliable and accurate intraoperative visualisation tools for minimally invasive surgery to improve surgical outcomes and enhance patient care. A recent miniaturised cancer detection probe (i.e., SENSEI developed by Lightpoint Medical Ltd.) leverages the cancer-targeting ability of nuclear agents to more accurately identify cancer intra-operatively using the emitted gamma signal. However, the use of this probe presents a visualisation challenge as the probe is non-imaging and is air-gapped from the tissue, making it challenging for the surgeon to locate the probe-sensing area on the tissue surface. Geometrically, the sensing area is defined as the intersection point between the gamma probe axis and the tissue surface in 3D space but projected onto the 2D laparoscopic image. Hence, in this thesis, tool tracking, pose estimation, and segmentation tools were developed first, followed by laparoscope image depth estimation algorithms and 3D reconstruction methods.

Are nuclear masks all you need for improved out-of-domain generalisation? A closer look at cancer classification in histopathology

Domain generalisation in computational histopathology is challenging because the images are substantially affected by differences among hospitals due to factors like fixation and staining of tissue and imaging equipment. We hypothesise that focusing on nuclei can improve the out-of-domain (OOD) generalisation in cancer detection. We propose a simple approach to improve OOD generalisation for cancer detection by focusing on nuclear morphology and organisation, as these are domain-invariant features critical in cancer detection. Our approach integrates original images with nuclear segmentation masks during training, encouraging the model to prioritise nuclei and their spatial arrangement. Going beyond mere data augmentation, we introduce a regularisation technique that aligns the representations of masks and original images. We show, using multiple datasets, that our method improves OOD generalisation and also leads to increased robustness to image corruptions and adversarial attacks. The source code is available at https://github.com/undercutspiky/SFL/

MSEG-VCUQ: Multimodal SEGmentation with Enhanced Vision Foundation Models, Convolutional Neural Networks, and Uncertainty Quantification for High-Speed Video Phase Detection Data

Purpose: High-speed video (HSV) phase detection (PD) segmentation is vital in nuclear reactors, chemical processing, and electronics cooling for detecting vapor, liquid, and microlayer phases. Traditional segmentation models face pixel-level accuracy and generalization issues in multimodal data. MSEG-VCUQ introduces VideoSAM, a hybrid framework leveraging convolutional neural networks (CNNs) and transformer-based vision models to enhance segmentation accuracy and generalizability across complex multimodal PD tasks. Methods: VideoSAM combines U-Net CNN and the Segment Anything Model (SAM) for advanced feature extraction and segmentation across diverse HSV PD modalities, spanning fluids like water, FC-72, nitrogen, and argon under varied heat flux conditions. The framework also incorporates uncertainty quantification (UQ) to assess pixel-based discretization errors, delivering reliable metrics such as contact line density and dry area fraction under experimental conditions. Results: VideoSAM outperforms SAM and modality-specific CNN models in segmentation accuracy, excelling in environments with complex phase boundaries, overlapping bubbles, and dynamic liquid-vapor interactions. Its hybrid architecture supports cross-dataset generalization, adapting effectively to varying modalities. The UQ module provides accurate error estimates, enhancing the reliability of segmentation outputs for advanced HSV PD research. Conclusion: MSEG-VCUQ, via VideoSAM, offers a robust solution for HSV PD segmentation, addressing previous limitations with advanced deep learning and UQ techniques. The open-source datasets and tools introduced enable scalable, precise, and adaptable segmentation for multimodal PD datasets, supporting advancements in HSV analysis and autonomous experimentation. The codes and data used for this paper are publicly available at: \url{https://github.com/chikap421/mseg_vcuq}

Irregular Tensor Low-Rank Representation for Hyperspectral Image Representation

Spectral variation is a common problem for hyperspectral image (HSI) representation. Low-rank tensor representation is an important approach to alleviate spectral variations. However, the spatial distribution of the HSI is always irregular, while the previous tensor low-rank representation methods can only be applied to the regular data cubes, which limits the performance. To remedy this issue, in this paper we propose a novel irregular tensor low-rank representation model. We first segment the HSI data into several irregular homogeneous regions. Then, we propose a novel irregular tensor low-rank representation method that can efficiently model the irregular 3D cubes. We further use a non-convex nuclear norm to pursue the low-rankness and introduce a negative global low-rank term that improves global consistency. This proposed model is finally formulated as a convex-concave optimization problem and solved by alternative augmented Lagrangian method. Through experiments on four public datasets, the proposed method outperforms the existing low-rank based HSI methods significantly. Code is available at: https://github.com/hb-studying/ITLRR.

Curvature Diversity-Driven Deformation and Domain Alignment for Point Cloud

Unsupervised Domain Adaptation (UDA) is crucial for reducing the need for extensive manual data annotation when training deep networks on point cloud data. A significant challenge of UDA lies in effectively bridging the domain gap. To tackle this challenge, we propose \textbf{C}urvature \textbf{D}iversity-Driven \textbf{N}uclear-Norm Wasserstein \textbf{D}omain Alignment (CDND). Our approach first introduces a \textit{\textbf{Curv}ature Diversity-driven Deformation \textbf{Rec}onstruction (CurvRec)} task, which effectively mitigates the gap between the source and target domains by enabling the model to extract salient features from semantically rich regions of a given point cloud. We then propose \textit{\textbf{D}eformation-based \textbf{N}uclear-norm \textbf{W}asserstein \textbf{D}iscrepancy (D-NWD)}, which applies the Nuclear-norm Wasserstein Discrepancy to both \textit{deformed and original} data samples to align the source and target domains. Furthermore, we contribute a theoretical justification for the effectiveness of D-NWD in distribution alignment and demonstrate that it is \textit{generic} enough to be applied to \textbf{any} deformations. To validate our method, we conduct extensive experiments on two public domain adaptation datasets for point cloud classification and segmentation tasks. Empirical experiment results show that our CDND achieves state-of-the-art performance by a noticeable margin over existing approaches.

On generalisability of segment anything model for nuclear instance segmentation in histology images

Pre-trained on a large and diverse dataset, the segment anything model (SAM) is the first promptable foundation model in computer vision aiming at object segmentation tasks. In this work, we evaluate SAM for the task of nuclear instance segmentation performance with zero-shot learning and finetuning. We compare SAM with other representative methods in nuclear instance segmentation, especially in the context of model generalisability. To achieve automatic nuclear instance segmentation, we propose using a nuclei detection model to provide bounding boxes or central points of nu-clei as visual prompts for SAM in generating nuclear instance masks from histology images.

Rethinking Annotator Simulation: Realistic Evaluation of Whole-Body PET Lesion Interactive Segmentation Methods

Interactive segmentation plays a crucial role in accelerating the annotation, particularly in domains requiring specialized expertise such as nuclear medicine. For example, annotating lesions in whole-body Positron Emission Tomography (PET) images can require over an hour per volume. While previous works evaluate interactive segmentation models through either real user studies or simulated annotators, both approaches present challenges. Real user studies are expensive and often limited in scale, while simulated annotators, also known as robot users, tend to overestimate model performance due to their idealized nature. To address these limitations, we introduce four evaluation metrics that quantify the user shift between real and simulated annotators. In an initial user study involving four annotators, we assess existing robot users using our proposed metrics and find that robot users significantly deviate in performance and annotation behavior compared to real annotators. Based on these findings, we propose a more realistic robot user that reduces the user shift by incorporating human factors such as click variation and inter-annotator disagreement. We validate our robot user in a second user study, involving four other annotators, and show it consistently reduces the simulated-to-real user shift compared to traditional robot users. By employing our robot user, we can conduct more large-scale and cost-efficient evaluations of interactive segmentation models, while preserving the fidelity of real user studies. Our implementation is based on MONAI Label and will be made publicly available.

Macroscale fracture surface segmentation via semi-supervised learning considering the structural similarity

To this date the safety assessment of materials, used for example in the nuclear power sector, commonly relies on a fracture mechanical analysis utilizing macroscopic concepts, where a global load quantity K or J is compared to the materials fracture toughness curve. Part of the experimental effort involved in these concepts is dedicated to the quantitative analysis of fracture surfaces. Within the scope of this study a methodology for the semi-supervised training of deep learning models for fracture surface segmentation on a macroscopic level was established. Therefore, three distinct and unique datasets were created to analyze the influence of structural similarity on the segmentation capability. The structural similarity differs due to the assessed materials and specimen, as well as imaging-induced variance due to fluctuations in image acquisition in different laboratories. The datasets correspond to typical isolated laboratory conditions, complex real-world circumstances, and a curated subset of the two. We implemented a weak-to-strong consistency regularization for semi-supervised learning. On the heterogeneous dataset we were able to train robust and well-generalizing models that learned feature representations from images across different domains without observing a significant drop in prediction quality. Furthermore, our approach reduced the number of labeled images required for training by a factor of 6. To demonstrate the success of our method and the benefit of our approach for the fracture mechanics assessment, we utilized the models for initial crack size measurements with the area average method. For the laboratory setting, the deep learning assisted measurements proved to have the same quality as manual measurements. For models trained on the heterogeneous dataset, very good measurement accuracies with mean deviations smaller than 1 % could be achieved...

Unleashing the Power of Prompt-driven Nucleus Instance Segmentation

Nuclear instance segmentation in histology images is crucial for a broad spectrum of clinical applications. Current prevailing nuclear instance segmentation algorithms rely on regression of nuclei contours, distance maps, watershed markers or a proxy nuclear representation of star-convex polygons. Consequently, these methods necessitate sophisticated post-processing operations to distinguish nuclei instances, which are commonly acknowledged to be error-prone and parameter-sensitive. Recently, the segment anything model (SAM) has earned attracted huge attention within the domain of medical image segmentation due to its impressive generalization ability and promptable property. Nevertheless, its potential on nuclear instance segmentation remains largely underexplored. In this paper, we present a novel prompt-driven framework that consists of a point prompter and a SAM for automatic nuclei instance segmentation. Specifically, the prompter learns to generate a unique point prompt for each nucleus while the SAM is fine tuned to output the corresponding mask of the cued nucleus. Furthermore, we propose to add adjacent nuclei as negative prompts to promote the model's ability to recognize overlapping nuclei. Without bells and whistles, our proposed method sets a new state-of-the-art performance on three challenging benchmarks. Our code is available at \textcolor{magenta}{\url{https://github.com/windygoo/PromptNucSeg}} .

Direct mineral content prediction from drill core images via transfer learning

Deep subsurface exploration is important for mining, oil and gas industries, as well as in the assessment of geological units for the disposal of chemical or nuclear waste, or the viability of geothermal energy systems. Typically, detailed examinations of subsurface formations or units are performed on cuttings or core materials extracted during drilling campaigns, as well as on geophysical borehole data, which provide detailed information about the petrophysical properties of the rocks. Depending on the volume of rock samples and the analytical program, the laboratory analysis and diagnostics can be very time-consuming. This study investigates the potential of utilizing machine learning, specifically convolutional neural networks (CNN), to assess the lithology and mineral content solely from analysis of drill core images, aiming to support and expedite the subsurface geological exploration. The paper outlines a comprehensive methodology, encompassing data preprocessing, machine learning methods, and transfer learning techniques. The outcome reveals a remarkable 96.7% accuracy in the classification of drill core segments into distinct formation classes. Furthermore, a CNN model was trained for the evaluation of mineral content using a learning data set from multidimensional log analysis data (silicate, total clay, carbonate). When benchmarked against laboratory XRD measurements on samples from the cores, both the advanced multidimensional log analysis model and the neural network approach developed here provide equally good performance. This work demonstrates that deep learning and particularly transfer learning can support extracting petrophysical properties, including mineral content and formation classification, from drill core images, thus offering a road map for enhancing model performance and data set quality in image-based analysis of drill cores.