Synomaly Noise and Multi-Stage Diffusion: A Novel Approach for Unsupervised Anomaly Detection in Ultrasound Imaging

Ultrasound (US) imaging is widely used in routine clinical practice due to its advantages of being radiation-free, cost-effective, and portable. However, the low reproducibility and quality of US images, combined with the scarcity of expert-level annotation, make the training of fully supervised segmentation models challenging. To address these issues, we propose a novel unsupervised anomaly detection framework based on a diffusion model that incorporates a synthetic anomaly (Synomaly) noise function and a multi-stage diffusion process. Synomaly noise introduces synthetic anomalies into healthy images during training, allowing the model to effectively learn anomaly removal. The multi-stage diffusion process is introduced to progressively denoise images, preserving fine details while improving the quality of anomaly-free reconstructions. The generated high-fidelity counterfactual healthy images can further enhance the interpretability of the segmentation models, as well as provide a reliable baseline for evaluating the extent of anomalies and supporting clinical decision-making. Notably, the unsupervised anomaly detection model is trained purely on healthy images, eliminating the need for anomalous training samples and pixel-level annotations. We validate the proposed approach on carotid US, brain MRI, and liver CT datasets. The experimental results demonstrate that the proposed framework outperforms existing state-of-the-art unsupervised anomaly detection methods, achieving performance comparable to fully supervised segmentation models in the US dataset. Additionally, ablation studies underline the importance of hyperparameter selection for Synomaly noise and the effectiveness of the multi-stage diffusion process in enhancing model performance.

SCRREAM : SCan, Register, REnder And Map:A Framework for Annotating Accurate and Dense 3D Indoor Scenes with a Benchmark

Traditionally, 3d indoor datasets have generally prioritized scale over ground-truth accuracy in order to obtain improved generalization. However, using these datasets to evaluate dense geometry tasks, such as depth rendering, can be problematic as the meshes of the dataset are often incomplete and may produce wrong ground truth to evaluate the details. In this paper, we propose SCRREAM, a dataset annotation framework that allows annotation of fully dense meshes of objects in the scene and registers camera poses on the real image sequence, which can produce accurate ground truth for both sparse 3D as well as dense 3D tasks. We show the details of the dataset annotation pipeline and showcase four possible variants of datasets that can be obtained from our framework with example scenes, such as indoor reconstruction and SLAM, scene editing & object removal, human reconstruction and 6d pose estimation. Recent pipelines for indoor reconstruction and SLAM serve as new benchmarks. In contrast to previous indoor dataset, our design allows to evaluate dense geometry tasks on eleven sample scenes against accurately rendered ground truth depth maps.

KaLDeX: Kalman Filter based Linear Deformable Cross Attention for Retina Vessel Segmentation

Background and Objective: In the realm of ophthalmic imaging, accurate vascular segmentation is paramount for diagnosing and managing various eye diseases. Contemporary deep learning-based vascular segmentation models rival human accuracy but still face substantial challenges in accurately segmenting minuscule blood vessels in neural network applications. Due to the necessity of multiple downsampling operations in the CNN models, fine details from high-resolution images are inevitably lost. The objective of this study is to design a structure to capture the delicate and small blood vessels. Methods: To address these issues, we propose a novel network (KaLDeX) for vascular segmentation leveraging a Kalman filter based linear deformable cross attention (LDCA) module, integrated within a UNet++ framework. Our approach is based on two key components: Kalman filter (KF) based linear deformable convolution (LD) and cross-attention (CA) modules. The LD module is designed to adaptively adjust the focus on thin vessels that might be overlooked in standard convolution. The CA module improves the global understanding of vascular structures by aggregating the detailed features from the LD module with the high level features from the UNet++ architecture. Finally, we adopt a topological loss function based on persistent homology to constrain the topological continuity of the segmentation. Results: The proposed method is evaluated on retinal fundus image datasets (DRIVE, CHASE_BD1, and STARE) as well as the 3mm and 6mm of the OCTA-500 dataset, achieving an average accuracy (ACC) of 97.25%, 97.77%, 97.85%, 98.89%, and 98.21%, respectively. Conclusions: Empirical evidence shows that our method outperforms the current best models on different vessel segmentation datasets. Our source code is available at: https://github.com/AIEyeSystem/KalDeX.

Extrapolating Prospective Glaucoma Fundus Images through Diffusion Model in Irregular Longitudinal Sequences

The utilization of longitudinal datasets for glaucoma progression prediction offers a compelling approach to support early therapeutic interventions. Predominant methodologies in this domain have primarily focused on the direct prediction of glaucoma stage labels from longitudinal datasets. However, such methods may not adequately encapsulate the nuanced developmental trajectory of the disease. To enhance the diagnostic acumen of medical practitioners, we propose a novel diffusion-based model to predict prospective images by extrapolating from existing longitudinal fundus images of patients. The methodology delineated in this study distinctively leverages sequences of images as inputs. Subsequently, a time-aligned mask is employed to select a specific year for image generation. During the training phase, the time-aligned mask resolves the issue of irregular temporal intervals in longitudinal image sequence sampling. Additionally, we utilize a strategy of randomly masking a frame in the sequence to establish the ground truth. This methodology aids the network in continuously acquiring knowledge regarding the internal relationships among the sequences throughout the learning phase. Moreover, the introduction of textual labels is instrumental in categorizing images generated within the sequence. The empirical findings from the conducted experiments indicate that our proposed model not only effectively generates longitudinal data but also significantly improves the precision of downstream classification tasks.

Neural Semantic Map-Learning for Autonomous Vehicles

Autonomous vehicles demand detailed maps to maneuver reliably through traffic, which need to be kept up-to-date to ensure a safe operation. A promising way to adapt the maps to the ever-changing road-network is to use crowd-sourced data from a fleet of vehicles. In this work, we present a mapping system that fuses local submaps gathered from a fleet of vehicles at a central instance to produce a coherent map of the road environment including drivable area, lane markings, poles, obstacles and more as a 3D mesh. Each vehicle contributes locally reconstructed submaps as lightweight meshes, making our method applicable to a wide range of reconstruction methods and sensor modalities. Our method jointly aligns and merges the noisy and incomplete local submaps using a scene-specific Neural Signed Distance Field, which is supervised using the submap meshes to predict a fused environment representation. We leverage memory-efficient sparse feature-grids to scale to large areas and introduce a confidence score to model uncertainty in scene reconstruction. Our approach is evaluated on two datasets with different local mapping methods, showing improved pose alignment and reconstruction over existing methods. Additionally, we demonstrate the benefit of multi-session mapping and examine the required amount of data to enable high-fidelity map learning for autonomous vehicles.

Intraoperative Registration by Cross-Modal Inverse Neural Rendering

We present in this paper a novel approach for 3D/2D intraoperative registration during neurosurgery via cross-modal inverse neural rendering. Our approach separates implicit neural representation into two components, handling anatomical structure preoperatively and appearance intraoperatively. This disentanglement is achieved by controlling a Neural Radiance Field's appearance with a multi-style hypernetwork. Once trained, the implicit neural representation serves as a differentiable rendering engine, which can be used to estimate the surgical camera pose by minimizing the dissimilarity between its rendered images and the target intraoperative image. We tested our method on retrospective patients' data from clinical cases, showing that our method outperforms state-of-the-art while meeting current clinical standards for registration. Code and additional resources can be found at https://maxfehrentz.github.io/style-ngp/.

SURGIVID: Annotation-Efficient Surgical Video Object Discovery

Surgical scenes convey crucial information about the quality of surgery. Pixel-wise localization of tools and anatomical structures is the first task towards deeper surgical analysis for microscopic or endoscopic surgical views. This is typically done via fully-supervised methods which are annotation greedy and in several cases, demanding medical expertise. Considering the profusion of surgical videos obtained through standardized surgical workflows, we propose an annotation-efficient framework for the semantic segmentation of surgical scenes. We employ image-based self-supervised object discovery to identify the most salient tools and anatomical structures in surgical videos. These proposals are further refined within a minimally supervised fine-tuning step. Our unsupervised setup reinforced with only 36 annotation labels indicates comparable localization performance with fully-supervised segmentation models. Further, leveraging surgical phase labels as weak labels can better guide model attention towards surgical tools, leading to $\sim 2\%$ improvement in tool localization. Extensive ablation studies on the CaDIS dataset validate the effectiveness of our proposed solution in discovering relevant surgical objects with minimal or no supervision.

MAGDA: Multi-agent guideline-driven diagnostic assistance

In emergency departments, rural hospitals, or clinics in less developed regions, clinicians often lack fast image analysis by trained radiologists, which can have a detrimental effect on patients' healthcare. Large Language Models (LLMs) have the potential to alleviate some pressure from these clinicians by providing insights that can help them in their decision-making. While these LLMs achieve high test results on medical exams showcasing their great theoretical medical knowledge, they tend not to follow medical guidelines. In this work, we introduce a new approach for zero-shot guideline-driven decision support. We model a system of multiple LLM agents augmented with a contrastive vision-language model that collaborate to reach a patient diagnosis. After providing the agents with simple diagnostic guidelines, they will synthesize prompts and screen the image for findings following these guidelines. Finally, they provide understandable chain-of-thought reasoning for their diagnosis, which is then self-refined to consider inter-dependencies between diseases. As our method is zero-shot, it is adaptable to settings with rare diseases, where training data is limited, but expert-crafted disease descriptions are available. We evaluate our method on two chest X-ray datasets, CheXpert and ChestX-ray 14 Longtail, showcasing performance improvement over existing zero-shot methods and generalizability to rare diseases.

Multimodal Analysis of White Blood Cell Differentiation in Acute Myeloid Leukemia Patients using a β-Variational Autoencoder

Biomedical imaging and RNA sequencing with single-cell resolution improves our understanding of white blood cell diseases like leukemia. By combining morphological and transcriptomic data, we can gain insights into cellular functions and trajectoriess involved in blood cell differentiation. However, existing methodologies struggle with integrating morphological and transcriptomic data, leaving a significant research gap in comprehensively understanding the dynamics of cell differentiation. Here, we introduce an unsupervised method that explores and reconstructs these two modalities and uncovers the relationship between different subtypes of white blood cells from human peripheral blood smears in terms of morphology and their corresponding transcriptome. Our method is based on a beta-variational autoencoder (\beta-VAE) with a customized loss function, incorporating a R-CNN architecture to distinguish single-cell from background and to minimize any interference from artifacts. This implementation of \beta-VAE shows good reconstruction capability along with continuous latent embeddings, while maintaining clear differentiation between single-cell classes. Our novel approach is especially helpful to uncover the correlation of two latent features in complex biological processes such as formation of granules in the cell (granulopoiesis) with gene expression patterns. It thus provides a unique tool to improve the understanding of white blood cell maturation for biomedicine and diagnostics.

PHOCUS: Physics-Based Deconvolution for Ultrasound Resolution Enhancement

Ultrasound is widely used in medical diagnostics allowing for accessible and powerful imaging but suffers from resolution limitations due to diffraction and the finite aperture of the imaging system, which restricts diagnostic use. The impulse function of an ultrasound imaging system is called the point spread function (PSF), which is convolved with the spatial distribution of reflectors in the image formation process. Recovering high-resolution reflector distributions by removing image distortions induced by the convolution process improves image clarity and detail. Conventionally, deconvolution techniques attempt to rectify the imaging system's dependent PSF, working directly on the radio-frequency (RF) data. However, RF data is often not readily accessible. Therefore, we introduce a physics-based deconvolution process using a modeled PSF, working directly on the more commonly available B-mode images. By leveraging Implicit Neural Representations (INRs), we learn a continuous mapping from spatial locations to their respective echogenicity values, effectively compensating for the discretized image space. Our contribution consists of a novel methodology for retrieving a continuous echogenicity map directly from a B-mode image through a differentiable physics-based rendering pipeline for ultrasound resolution enhancement. We qualitatively and quantitatively evaluate our approach on synthetic data, demonstrating improvements over traditional methods in metrics such as PSNR and SSIM. Furthermore, we show qualitative enhancements on an ultrasound phantom and an in-vivo acquisition of a carotid artery.