Step-Calibrated Diffusion for Biomedical Optical Image Restoration

High-quality, high-resolution medical imaging is essential for clinical care. Raman-based biomedical optical imaging uses non-ionizing infrared radiation to evaluate human tissues in real time and is used for early cancer detection, brain tumor diagnosis, and intraoperative tissue analysis. Unfortunately, optical imaging is vulnerable to image degradation due to laser scattering and absorption, which can result in diagnostic errors and misguided treatment. Restoration of optical images is a challenging computer vision task because the sources of image degradation are multi-factorial, stochastic, and tissue-dependent, preventing a straightforward method to obtain paired low-quality/high-quality data. Here, we present Restorative Step-Calibrated Diffusion (RSCD), an unpaired image restoration method that views the image restoration problem as completing the finishing steps of a diffusion-based image generation task. RSCD uses a step calibrator model to dynamically determine the severity of image degradation and the number of steps required to complete the reverse diffusion process for image restoration. RSCD outperforms other widely used unpaired image restoration methods on both image quality and perceptual evaluation metrics for restoring optical images. Medical imaging experts consistently prefer images restored using RSCD in blinded comparison experiments and report minimal to no hallucinations. Finally, we show that RSCD improves performance on downstream clinical imaging tasks, including automated brain tumor diagnosis and deep tissue imaging. Our code is available at https://github.com/MLNeurosurg/restorative_step-calibrated_diffusion.

Gaussian Pancakes: Geometrically-Regularized 3D Gaussian Splatting for Realistic Endoscopic Reconstruction

Within colorectal cancer diagnostics, conventional colonoscopy techniques face critical limitations, including a limited field of view and a lack of depth information, which can impede the detection of precancerous lesions. Current methods struggle to provide comprehensive and accurate 3D reconstructions of the colonic surface which can help minimize the missing regions and reinspection for pre-cancerous polyps. Addressing this, we introduce 'Gaussian Pancakes', a method that leverages 3D Gaussian Splatting (3D GS) combined with a Recurrent Neural Network-based Simultaneous Localization and Mapping (RNNSLAM) system. By introducing geometric and depth regularization into the 3D GS framework, our approach ensures more accurate alignment of Gaussians with the colon surface, resulting in smoother 3D reconstructions with novel viewing of detailed textures and structures. Evaluations across three diverse datasets show that Gaussian Pancakes enhances novel view synthesis quality, surpassing current leading methods with a 18% boost in PSNR and a 16% improvement in SSIM. It also delivers over 100X faster rendering and more than 10X shorter training times, making it a practical tool for real-time applications. Hence, this holds promise for achieving clinical translation for better detection and diagnosis of colorectal cancer.

Towards Enhanced Analysis of Lung Cancer Lesions in EBUS-TBNA -- A Semi-Supervised Video Object Detection Method

This study aims to establish a computer-aided diagnostic system for lung lesions using bronchoscope endobronchial ultrasound (EBUS) to assist physicians in identifying lesion areas. During EBUS-transbronchial needle aspiration (EBUS-TBNA) procedures, physicians rely on grayscale ultrasound images to determine the location of lesions. However, these images often contain significant noise and can be influenced by surrounding tissues or blood vessels, making interpretation challenging. Previous research has lacked the application of object detection models to EBUS-TBNA, and there has been no well-defined solution for annotating the EBUS-TBNA dataset. In related studies on ultrasound images, although models have been successful in capturing target regions for their respective tasks, their training and predictions have been based on two-dimensional images, limiting their ability to leverage temporal features for improved predictions. This study introduces a three-dimensional image-based object detection model. It utilizes an attention mechanism to capture temporal correlations and we will implements a filtering mechanism to select relevant information from previous frames. Subsequently, a teacher-student model training approach is employed to optimize the model further, leveraging unlabeled data. To mitigate the impact of poor-quality pseudo-labels on the student model, we will add a special Gaussian Mixture Model (GMM) to ensure the quality of pseudo-labels.

In-Vivo Hyperspectral Human Brain Image Database for Brain Cancer Detection

The use of hyperspectral imaging for medical applications is becoming more common in recent years. One of the main obstacles that researchers find when developing hyperspectral algorithms for medical applications is the lack of specific, publicly available, and hyperspectral medical data. The work described in this paper was developed within the framework of the European project HELICoiD (HypErspectraL Imaging Cancer Detection), which had as a main goal the application of hyperspectral imaging to the delineation of brain tumors in real-time during neurosurgical operations. In this paper, the methodology followed to generate the first hyperspectral database of in-vivo human brain tissues is presented. Data was acquired employing a customized hyperspectral acquisition system capable of capturing information in the Visual and Near InfraRed (VNIR) range from 400 to 1000 nm. Repeatability was assessed for the cases where two images of the same scene were captured consecutively. The analysis reveals that the system works more efficiently in the spectral range between 450 and 900 nm. A total of 36 hyperspectral images from 22 different patients were obtained. From these data, more than 300 000 spectral signatures were labeled employing a semi-automatic methodology based on the spectral angle mapper algorithm. Four different classes were defined: normal tissue, tumor tissue, blood vessel, and background elements. All the hyperspectral data has been made available in a public repository.

Distribution-informed and wavelength-flexible data-driven photoacoustic oximetry

Significance: Photoacoustic imaging (PAI) promises to measure spatially-resolved blood oxygen saturation, but suffers from a lack of accurate and robust spectral unmixing methods to deliver on this promise. Accurate blood oxygenation estimation could have important clinical applications, from cancer detection to quantifying inflammation. Aim: This study addresses the inflexibility of existing data-driven methods for estimating blood oxygenation in PAI by introducing a recurrent neural network architecture. Approach: We created 25 simulated training dataset variations to assess neural network performance. We used a long short-term memory network to implement a wavelength-flexible network architecture and proposed the Jensen-Shannon divergence to predict the most suitable training dataset. Results: The network architecture can handle arbitrary input wavelengths and outperforms linear unmixing and the previously proposed learned spectral decolouring method. Small changes in the training data significantly affect the accuracy of our method, but we find that the Jensen-Shannon divergence correlates with the estimation error and is thus suitable for predicting the most appropriate training datasets for any given application. Conclusions: A flexible data-driven network architecture combined with the Jensen-Shannon Divergence to predict the best training data set provides a promising direction that might enable robust data-driven photoacoustic oximetry for clinical use cases.

From Pixel to Cancer: Cellular Automata in Computed Tomography

AI for cancer detection encounters the bottleneck of data scarcity, annotation difficulty, and low prevalence of early tumors. Tumor synthesis seeks to create artificial tumors in medical images, which can greatly diversify the data and annotations for AI training. However, current tumor synthesis approaches are not applicable across different organs due to their need for specific expertise and design. This paper establishes a set of generic rules to simulate tumor development. Each cell (pixel) is initially assigned a state between zero and ten to represent the tumor population, and a tumor can be developed based on three rules to describe the process of growth, invasion, and death. We apply these three generic rules to simulate tumor development--from pixel to cancer--using cellular automata. We then integrate the tumor state into the original computed tomography (CT) images to generate synthetic tumors across different organs. This tumor synthesis approach allows for sampling tumors at multiple stages and analyzing tumor-organ interaction. Clinically, a reader study involving three expert radiologists reveals that the synthetic tumors and their developing trajectories are convincingly realistic. Technically, we generate tumors at varied stages in 9,262 raw, unlabeled CT images sourced from 68 hospitals worldwide. The performance in segmenting tumors in the liver, pancreas, and kidneys exceeds prevailing literature benchmarks, underlining the immense potential of tumor synthesis, especially for earlier cancer detection. The code and models are available at https://github.com/MrGiovanni/Pixel2Cancer

Web-based Melanoma Detection

Melanoma is the most aggressive form of skin cancer, and early detection can significantly increase survival rates and prevent cancer spread. However, developing reliable automated detection techniques is difficult due to the lack of standardized datasets and evaluation methods. This study introduces a unified melanoma classification approach that supports 54 combinations of 11 datasets and 24 state-of-the-art deep learning architectures. It enables a fair comparison of 1,296 experiments and results in a lightweight model deployable to the web-based MeshNet architecture named Mela-D. This approach can run up to 33x faster by reducing parameters 24x to yield an analogous 88.8\% accuracy comparable with ResNet50 on previously unseen images. This allows efficient and accurate melanoma detection in real-world settings that can run on consumer-level hardware.

XAI for Skin Cancer Detection with Prototypes and Non-Expert Supervision

Skin cancer detection through dermoscopy image analysis is a critical task. However, existing models used for this purpose often lack interpretability and reliability, raising the concern of physicians due to their black-box nature. In this paper, we propose a novel approach for the diagnosis of melanoma using an interpretable prototypical-part model. We introduce a guided supervision based on non-expert feedback through the incorporation of: 1) binary masks, obtained automatically using a segmentation network; and 2) user-refined prototypes. These two distinct information pathways aim to ensure that the learned prototypes correspond to relevant areas within the skin lesion, excluding confounding factors beyond its boundaries. Experimental results demonstrate that, even without expert supervision, our approach achieves superior performance and generalization compared to non-interpretable models.

Interpretable cancer cell detection with phonon microscopy using multi-task conditional neural networks for inter-batch calibration

Advances in artificial intelligence (AI) show great potential in revealing underlying information from phonon microscopy (high-frequency ultrasound) data to identify cancerous cells. However, this technology suffers from the 'batch effect' that comes from unavoidable technical variations between each experiment, creating confounding variables that the AI model may inadvertently learn. We therefore present a multi-task conditional neural network framework to simultaneously achieve inter-batch calibration, by removing confounding variables, and accurate cell classification of time-resolved phonon-derived signals. We validate our approach by training and validating on different experimental batches, achieving a balanced precision of 89.22% and an average cross-validated precision of 89.07% for classifying background, healthy and cancerous regions. Classification can be performed in 0.5 seconds with only simple prior batch information required for multiple batch corrections. Further, we extend our model to reconstruct denoised signals, enabling physical interpretation of salient features indicating disease state including sound velocity, sound attenuation and cell-adhesion to substrate.