Tobias Czempiel

Tobias Czempiel, Coco Rogers, Matthias Keicher et al. · stanford

Quantifying COVID-19 infection over time is an important task to manage the hospitalization of patients during a global pandemic. Recently, deep learning-based approaches have been proposed to help radiologists automatically quantify COVID-19 pathologies on longitudinal CT scans. However, the learning process of deep learning methods demands extensive training data to learn the complex characteristics of infected regions over longitudinal scans. It is challenging to collect a large-scale dataset, especially for longitudinal training. In this study, we want to address this problem by proposing a new self-supervised learning method to effectively train longitudinal networks for the quantification of COVID-19 infections. For this purpose, longitudinal self-supervision schemes are explored on clinical longitudinal COVID-19 CT scans. Experimental results show that the proposed method is effective, helping the model better exploit the semantics of longitudinal data and improve two COVID-19 quantification tasks.

Felix Holm, Ghazal Ghazaei, Tobias Czempiel et al.

Surgical videos captured from microscopic or endoscopic imaging devices are rich but complex sources of information, depicting different tools and anatomical structures utilized during an extended amount of time. Despite containing crucial workflow information and being commonly recorded in many procedures, usage of surgical videos for automated surgical workflow understanding is still limited. In this work, we exploit scene graphs as a more holistic, semantically meaningful and human-readable way to represent surgical videos while encoding all anatomical structures, tools, and their interactions. To properly evaluate the impact of our solutions, we create a scene graph dataset from semantic segmentations from the CaDIS and CATARACTS datasets. We demonstrate that scene graphs can be leveraged through the use of graph convolutional networks (GCNs) to tackle surgical downstream tasks such as surgical workflow recognition with competitive performance. Moreover, we demonstrate the benefits of surgical scene graphs regarding the explainability and robustness of model decisions, which are crucial in the clinical setting.

Chinedu Innocent Nwoye, Deepak Alapatt, Tong Yu et al.

Context-aware decision support in the operating room can foster surgical safety and efficiency by leveraging real-time feedback from surgical workflow analysis. Most existing works recognize surgical activities at a coarse-grained level, such as phases, steps or events, leaving out fine-grained interaction details about the surgical activity; yet those are needed for more helpful AI assistance in the operating room. Recognizing surgical actions as triplets of <instrument, verb, target> combination delivers comprehensive details about the activities taking place in surgical videos. This paper presents CholecTriplet2021: an endoscopic vision challenge organized at MICCAI 2021 for the recognition of surgical action triplets in laparoscopic videos. The challenge granted private access to the large-scale CholecT50 dataset, which is annotated with action triplet information. In this paper, we present the challenge setup and assessment of the state-of-the-art deep learning methods proposed by the participants during the challenge. A total of 4 baseline methods from the challenge organizers and 19 new deep learning algorithms by competing teams are presented to recognize surgical action triplets directly from surgical videos, achieving mean average precision (mAP) ranging from 4.2% to 38.1%. This study also analyzes the significance of the results obtained by the presented approaches, performs a thorough methodological comparison between them, in-depth result analysis, and proposes a novel ensemble method for enhanced recognition. Our analysis shows that surgical workflow analysis is not yet solved, and also highlights interesting directions for future research on fine-grained surgical activity recognition which is of utmost importance for the development of AI in surgery.

Tobias Czempiel, Aidean Sharghi, Magdalini Paschali et al. · stanford

Algorithmic surgical workflow recognition is an ongoing research field and can be divided into laparoscopic (Internal) and operating room (External) analysis. So far many different works for the internal analysis have been proposed with the combination of a frame-level and an additional temporal model to address the temporal ambiguities between different workflow phases. For the External recognition task, Clip-level methods are in the focus of researchers targeting the local ambiguities present in the OR scene. In this work we evaluate combinations of different model architectures for the task of surgical workflow recognition to provide a fair comparison of the methods for both Internal and External analysis. We show that methods designed for the Internal analysis can be transferred to the external task with comparable performance gains for different architectures.

Ege Özsoy, Evin Pınar Örnek, Ulrich Eck et al.

Surgical procedures are conducted in highly complex operating rooms (OR), comprising different actors, devices, and interactions. To date, only medically trained human experts are capable of understanding all the links and interactions in such a demanding environment. This paper aims to bring the community one step closer to automated, holistic and semantic understanding and modeling of OR domain. Towards this goal, for the first time, we propose using semantic scene graphs (SSG) to describe and summarize the surgical scene. The nodes of the scene graphs represent different actors and objects in the room, such as medical staff, patients, and medical equipment, whereas edges are the relationships between them. To validate the possibilities of the proposed representation, we create the first publicly available 4D surgical SSG dataset, 4D-OR, containing ten simulated total knee replacement surgeries recorded with six RGB-D sensors in a realistic OR simulation center. 4D-OR includes 6734 frames and is richly annotated with SSGs, human and object poses, and clinical roles. We propose an end-to-end neural network-based SSG generation pipeline, with a rate of success of 0.75 macro F1, indeed being able to infer semantic reasoning in the OR. We further demonstrate the representation power of our scene graphs by using it for the problem of clinical role prediction, where we achieve 0.85 macro F1. The code and dataset will be made available upon acceptance.

Chinedu Innocent Nwoye, Tong Yu, Saurav Sharma et al.

Formalizing surgical activities as triplets of the used instruments, actions performed, and target anatomies is becoming a gold standard approach for surgical activity modeling. The benefit is that this formalization helps to obtain a more detailed understanding of tool-tissue interaction which can be used to develop better Artificial Intelligence assistance for image-guided surgery. Earlier efforts and the CholecTriplet challenge introduced in 2021 have put together techniques aimed at recognizing these triplets from surgical footage. Estimating also the spatial locations of the triplets would offer a more precise intraoperative context-aware decision support for computer-assisted intervention. This paper presents the CholecTriplet2022 challenge, which extends surgical action triplet modeling from recognition to detection. It includes weakly-supervised bounding box localization of every visible surgical instrument (or tool), as the key actors, and the modeling of each tool-activity in the form of <instrument, verb, target> triplet. The paper describes a baseline method and 10 new deep learning algorithms presented at the challenge to solve the task. It also provides thorough methodological comparisons of the methods, an in-depth analysis of the obtained results across multiple metrics, visual and procedural challenges; their significance, and useful insights for future research directions and applications in surgery.

Alexander Saikia, Chiara Di Vece, Zhehua Mao et al.

Purpose: 3D reconstruction in minimally invasive surgery (MIS) enables enhanced surgical guidance through improved visualisation, tool tracking, and augmented reality. However, traditional RGB-based keypoint detection and matching pipelines struggle with surgical challenges, such as poor texture and complex illumination. We investigate whether using snapshot hyperspectral imaging (HSI) can provide improved results on keypoint detection and matching surgical scenes. Methods: We developed HyKey, a HYperspectral KEYpoint detection and description model made up of a hybrid 3D-2D convolutional neural network that jointly extracts spatial-spectral features from HSI. The model was trained using synthetic homographic augmentation and epipolar geometry constraints on a robotically-acquired dual-camera RGB-HSI laparoscopic dataset of ex-vivo organs with calibrated camera poses. We benchmarked performance against established RGB-based methods, including SuperPoint and ALIKE. Results: Our HSI-based model outperformed RGB baselines on registered RGB frames, achieving 96.62% mean matching accuracy and 67.18% mean average accuracy at 10 degree on pose estimation, demonstrating consistent improvements across multiple evaluation metrics. Conclusion: Integrating spectral information from an HSI cube offers a promising approach for robust monocular 3D reconstruction in MIS, addressing limitations of texture-poor surgical environments through enhanced spectral-spatial feature discrimination. Our model and dataset are available at https://github.com/alexsaikia/HyKey-Hyperspectral-Keypoint-Detection

Ege Özsoy, Tobias Czempiel, Felix Holm et al.

Modern surgeries are performed in complex and dynamic settings, including ever-changing interactions between medical staff, patients, and equipment. The holistic modeling of the operating room (OR) is, therefore, a challenging but essential task, with the potential to optimize the performance of surgical teams and aid in developing new surgical technologies to improve patient outcomes. The holistic representation of surgical scenes as semantic scene graphs (SGG), where entities are represented as nodes and relations between them as edges, is a promising direction for fine-grained semantic OR understanding. We propose, for the first time, the use of temporal information for more accurate and consistent holistic OR modeling. Specifically, we introduce memory scene graphs, where the scene graphs of previous time steps act as the temporal representation guiding the current prediction. We design an end-to-end architecture that intelligently fuses the temporal information of our lightweight memory scene graphs with the visual information from point clouds and images. We evaluate our method on the 4D-OR dataset and demonstrate that integrating temporality leads to more accurate and consistent results achieving an +5% increase and a new SOTA of 0.88 in macro F1. This work opens the path for representing the entire surgery history with memory scene graphs and improves the holistic understanding in the OR. Introducing scene graphs as memory representations can offer a valuable tool for many temporal understanding tasks.

Lennart Bastian, Tony Danjun Wang, Tobias Czempiel et al.

Purpose: Recent advances in Surgical Data Science (SDS) have contributed to an increase in video recordings from hospital environments. While methods such as surgical workflow recognition show potential in increasing the quality of patient care, the quantity of video data has surpassed the scale at which images can be manually anonymized. Existing automated 2D anonymization methods under-perform in Operating Rooms (OR), due to occlusions and obstructions. We propose to anonymize multi-view OR recordings using 3D data from multiple camera streams. Methods: RGB and depth images from multiple cameras are fused into a 3D point cloud representation of the scene. We then detect each individual's face in 3D by regressing a parametric human mesh model onto detected 3D human keypoints and aligning the face mesh with the fused 3D point cloud. The mesh model is rendered into every acquired camera view, replacing each individual's face. Results: Our method shows promise in locating faces at a higher rate than existing approaches. DisguisOR produces geometrically consistent anonymizations for each camera view, enabling more realistic anonymization that is less detrimental to downstream tasks. Conclusion: Frequent obstructions and crowding in operating rooms leaves significant room for improvement for off-the-shelf anonymization methods. DisguisOR addresses privacy on a scene level and has the potential to facilitate further research in SDS.

Dominik Batić, Felix Holm, Ege Özsoy et al.

Automated endoscopy video analysis is a challenging task in medical computer vision, with the primary objective of assisting surgeons during procedures. The difficulty arises from the complexity of surgical scenes and the lack of a sufficient amount of annotated data. In recent years, large-scale pretraining has shown great success in natural language processing and computer vision communities. These approaches reduce the need for annotated data, which is always a concern in the medical domain. However, most works on endoscopic video understanding use models pretrained on natural images, creating a domain gap between pretraining and finetuning. In this work, we investigate the need for endoscopy domain-specific pretraining based on downstream objectives. To this end, we first collect Endo700k, the largest publicly available corpus of endoscopic images, extracted from nine public Minimally Invasive Surgery (MIS) datasets. Endo700k comprises more than 700,000 unannotated raw images. Next, we introduce EndoViT, an endoscopy pretrained Vision Transformer (ViT). Through ablations, we demonstrate that domain-specific pretraining is particularly beneficial for more complex downstream tasks, such as Action Triplet Detection, and less effective and even unnecessary for simpler tasks, such as Surgical Phase Recognition. We will release both our code and pretrained models upon acceptance to facilitate further research in this direction.

Lennart Bastian, Tobias Czempiel, Christian Heiliger et al.

The surgical operating room (OR) presents many opportunities for automation and optimization. Videos from various sources in the OR are becoming increasingly available. The medical community seeks to leverage this wealth of data to develop automated methods to advance interventional care, lower costs, and improve overall patient outcomes. Existing datasets from OR room cameras are thus far limited in size or modalities acquired, leaving it unclear which sensor modalities are best suited for tasks such as recognizing surgical action from videos. This study demonstrates that surgical action recognition performance can vary depending on the image modalities used. We perform a methodical analysis on several commonly available sensor modalities, presenting two fusion approaches that improve classification performance. The analyses are carried out on a set of multi-view RGB-D video recordings of 18 laparoscopic procedures.

Ege Özsoy, Felix Holm, Mahdi Saleh et al.

Scene Graph Generation (SGG) is a visual understanding task, aiming to describe a scene as a graph of entities and their relationships with each other. Existing works rely on location labels in form of bounding boxes or segmentation masks, increasing annotation costs and limiting dataset expansion. Recognizing that many applications do not require location data, we break this dependency and introduce location-free scene graph generation (LF-SGG). This new task aims at predicting instances of entities, as well as their relationships, without the explicit calculation of their spatial localization. To objectively evaluate the task, the predicted and ground truth scene graphs need to be compared. We solve this NP-hard problem through an efficient branching algorithm. Additionally, we design the first LF-SGG method, Pix2SG, using autoregressive sequence modeling. We demonstrate the effectiveness of our method on three scene graph generation datasets as well as two downstream tasks, image retrieval and visual question answering, and show that our approach is competitive to existing methods while not relying on location cues.

Matthias Keicher, Kamilia Zaripova, Tobias Czempiel et al.

The automation of chest X-ray reporting has garnered significant interest due to the time-consuming nature of the task. However, the clinical accuracy of free-text reports has proven challenging to quantify using natural language processing metrics, given the complexity of medical information, the variety of writing styles, and the potential for typos and inconsistencies. Structured reporting and standardized reports, on the other hand, can provide consistency and formalize the evaluation of clinical correctness. However, high-quality annotations for structured reporting are scarce. Therefore, we propose a method to predict clinical findings defined by sentences in structured reporting templates, which can be used to fill such templates. The approach involves training a contrastive language-image model using chest X-rays and related free-text radiological reports, then creating textual prompts for each structured finding and optimizing a classifier to predict clinical findings in the medical image. Results show that even with limited image-level annotations for training, the method can accomplish the structured reporting tasks of severity assessment of cardiomegaly and localizing pathologies in chest X-rays.

Ege Özsoy, Chantal Pellegrini, Tobias Czempiel et al.

Operating rooms (ORs) are complex, high-stakes environments requiring precise understanding of interactions among medical staff, tools, and equipment for enhancing surgical assistance, situational awareness, and patient safety. Current datasets fall short in scale, realism and do not capture the multimodal nature of OR scenes, limiting progress in OR modeling. To this end, we introduce MM-OR, a realistic and large-scale multimodal spatiotemporal OR dataset, and the first dataset to enable multimodal scene graph generation. MM-OR captures comprehensive OR scenes containing RGB-D data, detail views, audio, speech transcripts, robotic logs, and tracking data and is annotated with panoptic segmentations, semantic scene graphs, and downstream task labels. Further, we propose MM2SG, the first multimodal large vision-language model for scene graph generation, and through extensive experiments, demonstrate its ability to effectively leverage multimodal inputs. Together, MM-OR and MM2SG establish a new benchmark for holistic OR understanding, and open the path towards multimodal scene analysis in complex, high-stakes environments. Our code, and data is available at https://github.com/egeozsoy/MM-OR.

Tobias Czempiel, Alfie Roddan, Maria Leiloglou et al.

This study investigates the reconstruction of hyperspectral signatures from RGB data to enhance surgical imaging, utilizing the publicly available HeiPorSPECTRAL dataset from porcine surgery and an in-house neurosurgery dataset. Various architectures based on convolutional neural networks (CNNs) and transformer models are evaluated using comprehensive metrics. Transformer models exhibit superior performance in terms of RMSE, SAM, PSNR and SSIM by effectively integrating spatial information to predict accurate spectral profiles, encompassing both visible and extended spectral ranges. Qualitative assessments demonstrate the capability to predict spectral profiles critical for informed surgical decision-making during procedures. Challenges associated with capturing both the visible and extended hyperspectral ranges are highlighted using the MAE, emphasizing the complexities involved. The findings open up the new research direction of hyperspectral reconstruction for surgical applications and clinical use cases in real-time surgical environments.

Tony Danjun Wang, Lennart Bastian, Tobias Czempiel et al.

Surgical domain models improve workflow optimization through automated predictions of each staff member's surgical role. However, mounting evidence indicates that team familiarity and individuality impact surgical outcomes. We present a novel staff-centric modeling approach that characterizes individual team members through their distinctive movement patterns and physical characteristics, enabling long-term tracking and analysis of surgical personnel across multiple procedures. To address the challenge of inter-clinic variability, we develop a generalizable re-identification framework that encodes sequences of 3D point clouds to capture shape and articulated motion patterns unique to each individual. Our method achieves 86.19% accuracy on realistic clinical data while maintaining 75.27% accuracy when transferring between different environments - a 12% improvement over existing methods. When used to augment markerless personnel tracking, our approach improves accuracy by over 50%. Through extensive validation across three datasets and the introduction of a novel workflow visualization technique, we demonstrate how our framework can reveal novel insights into surgical team dynamics and space utilization patterns, advancing methods to analyze surgical workflows and team coordination.

Alexander Saikia, Chiara Di Vece, Sierra Bonilla et al.

Minimally invasive surgery (MIS) offers significant benefits such as reduced recovery time and minimised patient trauma, but poses challenges in visibility and access, making accurate 3D reconstruction a significant tool in surgical planning and navigation. This work introduces a robotic arm platform for efficient multi-view image acquisition and precise 3D reconstruction in MIS settings. We adapted a laparoscope to a robotic arm and captured ex-vivo images of several ovine organs across varying lighting conditions (operating room and laparoscopic) and trajectories (spherical and laparoscopic). We employed recently released learning-based feature matchers combined with COLMAP to produce our reconstructions. The reconstructions were evaluated against high-precision laser scans for quantitative evaluation. Our results show that whilst reconstructions suffer most under realistic MIS lighting and trajectory, many versions of our pipeline achieve close to sub-millimetre accuracy with an average of 1.05 mm Root Mean Squared Error and 0.82 mm Chamfer distance. Our best reconstruction results occur with operating room lighting and spherical trajectories. Our robotic platform provides a tool for controlled, repeatable multi-view data acquisition for 3D generation in MIS environments which we hope leads to new datasets for training learning-based models.

Tony Danjun Wang, Tobias Czempiel, Nassir Navab et al.

Deep neural networks are prone to learning spurious correlations, exploiting dataset-specific artifacts rather than meaningful features for prediction. In surgical operating rooms (OR), these manifest through the standardization of smocks and gowns that obscure robust identifying landmarks, introducing model bias for tasks related to modeling OR personnel. Through gradient-based saliency analysis on two public OR datasets, we reveal that CNN models succumb to such shortcuts, fixating on incidental visual cues such as footwear beneath surgical gowns, distinctive eyewear, or other role-specific identifiers. Avoiding such biases is essential for the next generation of intelligent assistance systems in the OR, which should accurately recognize personalized workflow traits, such as surgical skill level or coordination with other staff members. We address this problem by encoding personnel as 3D point cloud sequences, disentangling identity-relevant shape and motion patterns from appearance-based confounders. Our experiments demonstrate that while RGB and geometric methods achieve comparable performance on datasets with apparent simulation artifacts, RGB models suffer a 12% accuracy drop in realistic clinical settings with decreased visual diversity due to standardizations. This performance gap confirms that geometric representations capture more meaningful biometric features, providing an avenue to developing robust methods of modeling humans in the OR.

Alfie Roddan, Tobias Czempiel, Chi Xu et al.

We present SAMSA 2.0, an interactive segmentation framework for hyperspectral medical imaging that introduces spectral angle prompting to guide the Segment Anything Model (SAM) using spectral similarity alongside spatial cues. This early fusion of spectral information enables more accurate and robust segmentation across diverse spectral datasets. Without retraining, SAMSA 2.0 achieves up to +3.8% higher Dice scores compared to RGB-only models and up to +3.1% over prior spectral fusion methods. Our approach enhances few-shot and zero-shot performance, demonstrating strong generalization in challenging low-data and noisy scenarios common in clinical imaging.

Alfie Roddan, Tobias Czempiel, Chi Xu et al.

Hyperspectral imaging (HSI) provides rich spectral information for medical imaging, yet encounters significant challenges due to data limitations and hardware variations. We introduce SAMSA, a novel interactive segmentation framework that combines an RGB foundation model with spectral analysis. SAMSA efficiently utilizes user clicks to guide both RGB segmentation and spectral similarity computations. The method addresses key limitations in HSI segmentation through a unique spectral feature fusion strategy that operates independently of spectral band count and resolution. Performance evaluation on publicly available datasets has shown 81.0% 1-click and 93.4% 5-click DICE on a neurosurgical and 81.1% 1-click and 89.2% 5-click DICE on an intraoperative porcine hyperspectral dataset. Experimental results demonstrate SAMSA's effectiveness in few-shot and zero-shot learning scenarios and using minimal training examples. Our approach enables seamless integration of datasets with different spectral characteristics, providing a flexible framework for hyperspectral medical image analysis.

Matthias Keicher, Hendrik Burwinkel, David Bani-Harouni et al.

During the first wave of COVID-19, hospitals were overwhelmed with the high number of admitted patients. An accurate prediction of the most likely individual disease progression can improve the planning of limited resources and finding the optimal treatment for patients. However, when dealing with a newly emerging disease such as COVID-19, the impact of patient- and disease-specific factors (e.g. body weight or known co-morbidities) on the immediate course of disease is by and large unknown. In the case of COVID-19, the need for intensive care unit (ICU) admission of pneumonia patients is often determined only by acute indicators such as vital signs (e.g. breathing rate, blood oxygen levels), whereas statistical analysis and decision support systems that integrate all of the available data could enable an earlier prognosis. To this end, we propose a holistic graph-based approach combining both imaging and non-imaging information. Specifically, we introduce a multimodal similarity metric to build a population graph for clustering patients and an image-based end-to-end Graph Attention Network to process this graph and predict the COVID-19 patient outcomes: admission to ICU, need for ventilation and mortality. Additionally, the network segments chest CT images as an auxiliary task and extracts image features and radiomics for feature fusion with the available metadata. Results on a dataset collected in Klinikum rechts der Isar in Munich, Germany show that our approach outperforms single modality and non-graph baselines. Moreover, our clustering and graph attention allow for increased understanding of the patient relationships within the population graph and provide insight into the network's decision-making process.

Seong Tae Kim, Leili Goli, Magdalini Paschali et al.

Chest computed tomography (CT) has played an essential diagnostic role in assessing patients with COVID-19 by showing disease-specific image features such as ground-glass opacity and consolidation. Image segmentation methods have proven to help quantify the disease burden and even help predict the outcome. The availability of longitudinal CT series may also result in an efficient and effective method to reliably assess the progression of COVID-19, monitor the healing process and the response to different therapeutic strategies. In this paper, we propose a new framework to identify infection at a voxel level (identification of healthy lung, consolidation, and ground-glass opacity) and visualize the progression of COVID-19 using sequential low-dose non-contrast CT scans. In particular, we devise a longitudinal segmentation network that utilizes the reference scan information to improve the performance of disease identification. Experimental results on a clinical longitudinal dataset collected in our institution show the effectiveness of the proposed method compared to the static deep neural networks for disease quantification.

Tobias Czempiel, Magdalini Paschali, Daniel Ostler et al.

In this paper we introduce OperA, a transformer-based model that accurately predicts surgical phases from long video sequences. A novel attention regularization loss encourages the model to focus on high-quality frames during training. Moreover, the attention weights are utilized to identify characteristic high attention frames for each surgical phase, which could further be used for surgery summarization. OperA is thoroughly evaluated on two datasets of laparoscopic cholecystectomy videos, outperforming various state-of-the-art temporal refinement approaches.

Tobias Czempiel, Magdalini Paschali, Matthias Keicher et al.

Automatic surgical phase recognition is a challenging and crucial task with the potential to improve patient safety and become an integral part of intra-operative decision-support systems. In this paper, we propose, for the first time in workflow analysis, a Multi-Stage Temporal Convolutional Network (MS-TCN) that performs hierarchical prediction refinement for surgical phase recognition. Causal, dilated convolutions allow for a large receptive field and online inference with smooth predictions even during ambiguous transitions. Our method is thoroughly evaluated on two datasets of laparoscopic cholecystectomy videos with and without the use of additional surgical tool information. Outperforming various state-of-the-art LSTM approaches, we verify the suitability of the proposed causal MS-TCN for surgical phase recognition.