SimuScope: Realistic Endoscopic Synthetic Dataset Generation through Surgical Simulation and Diffusion Models

Computer-assisted surgical (CAS) systems enhance surgical execution and outcomes by providing advanced support to surgeons. These systems often rely on deep learning models trained on complex, challenging-to-annotate data. While synthetic data generation can address these challenges, enhancing the realism of such data is crucial. This work introduces a multi-stage pipeline for generating realistic synthetic data, featuring a fully-fledged surgical simulator that automatically produces all necessary annotations for modern CAS systems. This simulator generates a wide set of annotations that surpass those available in public synthetic datasets. Additionally, it offers a more complex and realistic simulation of surgical interactions, including the dynamics between surgical instruments and deformable anatomical environments, outperforming existing approaches. To further bridge the visual gap between synthetic and real data, we propose a lightweight and flexible image-to-image translation method based on Stable Diffusion (SD) and Low-Rank Adaptation (LoRA). This method leverages a limited amount of annotated data, enables efficient training, and maintains the integrity of annotations generated by our simulator. The proposed pipeline is experimentally validated and can translate synthetic images into images with real-world characteristics, which can generalize to real-world context, thereby improving both training and CAS guidance. The code and the dataset are available at https://github.com/SanoScience/SimuScope.

PR-ENDO: Physically Based Relightable Gaussian Splatting for Endoscopy

Endoscopic procedures are crucial for colorectal cancer diagnosis, and three-dimensional reconstruction of the environment for real-time novel-view synthesis can significantly enhance diagnosis. We present PR-ENDO, a framework that leverages 3D Gaussian Splatting within a physically based, relightable model tailored for the complex acquisition conditions in endoscopy, such as restricted camera rotations and strong view-dependent illumination. By exploiting the connection between the camera and light source, our approach introduces a relighting model to capture the intricate interactions between light and tissue using physically based rendering and MLP. Existing methods often produce artifacts and inconsistencies under these conditions, which PR-ENDO overcomes by incorporating a specialized diffuse MLP that utilizes light angles and normal vectors, achieving stable reconstructions even with limited training camera rotations. We benchmarked our framework using a publicly available dataset and a newly introduced dataset with wider camera rotations. Our methods demonstrated superior image quality compared to baseline approaches.

Mediffusion: Joint Diffusion for Self-Explainable Semi-Supervised Classification and Medical Image Generation

We introduce Mediffusion -- a new method for semi-supervised learning with explainable classification based on a joint diffusion model. The medical imaging domain faces unique challenges due to scarce data labelling -- insufficient for standard training, and critical nature of the applications that require high performance, confidence, and explainability of the models. In this work, we propose to tackle those challenges with a single model that combines standard classification with a diffusion-based generative task in a single shared parametrisation. By sharing representations, our model effectively learns from both labeled and unlabeled data while at the same time providing accurate explanations through counterfactual examples. In our experiments, we show that our Mediffusion achieves results comparable to recent semi-supervised methods while providing more reliable and precise explanations.

TabMixer: Noninvasive Estimation of the Mean Pulmonary Artery Pressure via Imaging and Tabular Data Mixing

Right Heart Catheterization is a gold standard procedure for diagnosing Pulmonary Hypertension by measuring mean Pulmonary Artery Pressure (mPAP). It is invasive, costly, time-consuming and carries risks. In this paper, for the first time, we explore the estimation of mPAP from videos of noninvasive Cardiac Magnetic Resonance Imaging. To enhance the predictive capabilities of Deep Learning models used for this task, we introduce an additional modality in the form of demographic features and clinical measurements. Inspired by all-Multilayer Perceptron architectures, we present TabMixer, a novel module enabling the integration of imaging and tabular data through spatial, temporal and channel mixing. Specifically, we present the first approach that utilizes Multilayer Perceptrons to interchange tabular information with imaging features in vision models. We test TabMixer for mPAP estimation and show that it enhances the performance of Convolutional Neural Networks, 3D-MLP and Vision Transformers while being competitive with previous modules for imaging and tabular data. Our approach has the potential to improve clinical processes involving both modalities, particularly in noninvasive mPAP estimation, thus, significantly enhancing the quality of life for individuals affected by Pulmonary Hypertension. We provide a source code for using TabMixer at https://github.com/SanoScience/TabMixer.

Let Me DeCode You: Decoder Conditioning with Tabular Data

Training deep neural networks for 3D segmentation tasks can be challenging, often requiring efficient and effective strategies to improve model performance. In this study, we introduce a novel approach, DeCode, that utilizes label-derived features for model conditioning to support the decoder in the reconstruction process dynamically, aiming to enhance the efficiency of the training process. DeCode focuses on improving 3D segmentation performance through the incorporation of conditioning embedding with learned numerical representation of 3D-label shape features. Specifically, we develop an approach, where conditioning is applied during the training phase to guide the network toward robust segmentation. When labels are not available during inference, our model infers the necessary conditioning embedding directly from the input data, thanks to a feed-forward network learned during the training phase. This approach is tested using synthetic data and cone-beam computed tomography (CBCT) images of teeth. For CBCT, three datasets are used: one publicly available and two in-house. Our results show that DeCode significantly outperforms traditional, unconditioned models in terms of generalization to unseen data, achieving higher accuracy at a reduced computational cost. This work represents the first of its kind to explore conditioning strategies in 3D data segmentation, offering a novel and more efficient method for leveraging annotated data. Our code, pre-trained models are publicly available at https://github.com/SanoScience/DeCode .

TabAttention: Learning Attention Conditionally on Tabular Data

Medical data analysis often combines both imaging and tabular data processing using machine learning algorithms. While previous studies have investigated the impact of attention mechanisms on deep learning models, few have explored integrating attention modules and tabular data. In this paper, we introduce TabAttention, a novel module that enhances the performance of Convolutional Neural Networks (CNNs) with an attention mechanism that is trained conditionally on tabular data. Specifically, we extend the Convolutional Block Attention Module to 3D by adding a Temporal Attention Module that uses multi-head self-attention to learn attention maps. Furthermore, we enhance all attention modules by integrating tabular data embeddings. Our approach is demonstrated on the fetal birth weight (FBW) estimation task, using 92 fetal abdominal ultrasound video scans and fetal biometry measurements. Our results indicate that TabAttention outperforms clinicians and existing methods that rely on tabular and/or imaging data for FBW prediction. This novel approach has the potential to improve computer-aided diagnosis in various clinical workflows where imaging and tabular data are combined. We provide a source code for integrating TabAttention in CNNs at https://github.com/SanoScience/Tab-Attention.

Virtual Reality Simulator for Fetoscopic Spina Bifida Repair Surgery

Spina Bifida (SB) is a birth defect developed during the early stage of pregnancy in which there is incomplete closing of the spine around the spinal cord. The growing interest in fetoscopic Spina-Bifida repair, which is performed in fetuses who are still in the pregnant uterus, prompts the need for appropriate training. The learning curve for such procedures is steep and requires excellent procedural skills. Computer-based virtual reality (VR) simulation systems offer a safe, cost-effective, and configurable training environment free from ethical and patient safety issues. However, to the best of our knowledge, there are currently no commercial or experimental VR training simulation systems available for fetoscopic SB-repair procedures. In this paper, we propose a novel VR simulator for core manual skills training for SB-repair. An initial simulation realism validation study was carried out by obtaining subjective feedback (face and content validity) from 14 clinicians. The overall simulation realism was on average marked 4.07 on a 5-point Likert scale (1 - very unrealistic, 5 - very realistic). Its usefulness as a training tool for SB-repair as well as in learning fundamental laparoscopic skills was marked 4.63 and 4.80, respectively. These results indicate that VR simulation of fetoscopic procedures may contribute to surgical training without putting fetuses and their mothers at risk. It could also facilitate wider adaptation of fetoscopic procedures in place of much more invasive open fetal surgeries.