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A sensitivity increase of two orders of magnitude in proton (1H) and carbon (13C) spins via dynamic nuclear polarization (DNP) has been accomplished recently using a compact benchtop DNP polarizer operating at 1 T and 77 K. However the DNP mechanisms at play at such low magnetic field and high operating temperature are still not elucidated. A deeper understanding of the dominant polarization transfer mechanisms between electrons and 1H and 13C spins at these unconventional benchtop conditions is therefore required if one wants to devise strategies to boost sensitivity further. In this study, we found that DNP is generally dominated by solid effect for narrow electron paramagnetic resonance (EPR) line radicals (15 mM trityl OX063) and cross effect for broad EPR line radicals (50 mM TEMPOL). For both radicals, the dominant DNP mechanisms were investigated varying the microwave frequency and measuring the 1H and 13C DNP enhancement factors to obtain 1H and 13C DNP spectra. The impact of varying the microwave power on the 1H DNP buildup times and the 1H nuclear spin relaxation times were important as well to distinguish between solid effect and cross effect DNP. Finally, time-resolved electron saturation simulations under continuous microwave irradiation could replicate the experimental 1H and 13C DNP spectra at 1 T and 77 K for both radicals considering their electron relaxation properties. Only for trityl OX063, the 13C DNP spectra showed additional DNP maxima compared to the simulations. This has been attributed to methyl rotor induced 1H-13C heteronuclear cross relaxation in [1-13C] acetate present at 1 T and 77 K., Comment: Main text, 15 pages, 6 figures. Supporting information, 7 pages, 5 figures

Tomography of single-particle-resolved detectors is of primary importance for characterizing particle correlations with applications in quantum metrology, quantum simulation and quantum computing. However, it is a non-trivial task in practice due to the unavoidable presence of noise that affects the measurement but does not originate from the detector. In this work, we address this problem for a three-dimensional single-atom-resolved detector where shot-to-shot atom number fluctuations are a central issue to perform a quantum detector tomography. We overcome this difficulty by exploiting the parallel measurement of counting statistics in sub-volumes of the detector, from which we evaluate the effect of shot-to-shot fluctuations and perform a local tomography of the detector. In addition, we illustrate the validity of our method from applying it to Gaussian quantum states with different number statistics. Finally, we show that the response of Micro-Channel Plate detectors is well-described from using a binomial distribution with the detection efficiency as a single parameter., Comment: 7 pages, 5 figures

This paper introduces a novel pipeline designed to bring ultrasound (US) plane pose estimation closer to clinical use for more effective navigation to the standard planes (SPs) in the fetal brain. We propose a semi-supervised segmentation model utilizing both labeled SPs and unlabeled 3D US volume slices. Our model enables reliable segmentation across a diverse set of fetal brain images. Furthermore, the model incorporates a classification mechanism to identify the fetal brain precisely. Our model not only filters out frames lacking the brain but also generates masks for those containing it, enhancing the relevance of plane pose regression in clinical settings. We focus on fetal brain navigation from 2D ultrasound (US) video analysis and combine this model with a US plane pose regression network to provide sensorless proximity detection to SPs and non-SPs planes; we emphasize the importance of proximity detection to SPs for guiding sonographers, offering a substantial advantage over traditional methods by allowing earlier and more precise adjustments during scanning. We demonstrate the practical applicability of our approach through validation on real fetal scan videos obtained from sonographers of varying expertise levels. Our findings demonstrate the potential of our approach to complement existing fetal US technologies and advance prenatal diagnostic practices., Comment: 11 pages, 5 figures

The combination of a powerful and broadly applicable nuclear hyperpolarization technique with emerging (near-)zero-field modalities offer novel opportunities in a broad range of nuclear magnetic resonance spectroscopy and imaging applications, including biomedical diagnostics, monitoring catalytic reactions within metal reactors and many others. These are discussed along with a roadmap for future developments., Comment: 12 pages, 5 figures

Accurate spectroscopic measurements of calculable systems provide a powerful method for testing the Standard Model and extracting fundamental constants. Recently, spectroscopic measurements of finite nuclear size effects in normal and muonic hydrogen resulted in unexpectedly large adjustments of the proton charge radius and the Rydberg constant. We measured the $2^3\mathrm{S}\rightarrow2^1\mathrm{S}$ transition frequency in a Fermi gas of $^3$He with an order of magnitude higher accuracy than before. Together with a previous measurement in a $^4$He Bose-Einstein condensate, a squared charge radius difference $r^2_h - r^2_{\alpha} = 1.0757(15)\ \mathrm{fm^2}$ is determined between the helion and alpha particle. This measurement provides a benchmark with unprecedented accuracy for nuclear structure calculations. A deviation of 3.6$\sigma$ is found with a determination (arXiv:2305.11679) based on spectroscopy of muonic helium ions., Comment: Paper and supplementary in total 13 pages and 5 figures

International benchmarking competitions have become fundamental for the comparative performance assessment of image analysis methods. However, little attention has been given to investigating what can be learnt from these competitions. Do they really generate scientific progress? What are common and successful participation strategies? What makes a solution superior to a competing method? To address this gap in the literature, we performed a multi-center study with all 80 competitions that were conducted in the scope of IEEE ISBI 2021 and MICCAI 2021. Statistical analyses performed based on comprehensive descriptions of the submitted algorithms linked to their rank as well as the underlying participation strategies revealed common characteristics of winning solutions. These typically include the use of multi-task learning (63%) and/or multi-stage pipelines (61%), and a focus on augmentation (100%), image preprocessing (97%), data curation (79%), and postprocessing (66%). The "typical" lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning. Two core general development strategies stood out for highly-ranked teams: the reflection of the metrics in the method design and the focus on analyzing and handling failure cases. According to the organizers, 43% of the winning algorithms exceeded the state of the art but only 11% completely solved the respective domain problem. The insights of our study could help researchers (1) improve algorithm development strategies when approaching new problems, and (2) focus on open research questions revealed by this work., Comment: accepted to CVPR 2023

Validation metrics are key for the reliable tracking of scientific progress and for bridging the current chasm between artificial intelligence (AI) research and its translation into practice. However, increasing evidence shows that particularly in image analysis, metrics are often chosen inadequately in relation to the underlying research problem. This could be attributed to a lack of accessibility of metric-related knowledge: While taking into account the individual strengths, weaknesses, and limitations of validation metrics is a critical prerequisite to making educated choices, the relevant knowledge is currently scattered and poorly accessible to individual researchers. Based on a multi-stage Delphi process conducted by a multidisciplinary expert consortium as well as extensive community feedback, the present work provides the first reliable and comprehensive common point of access to information on pitfalls related to validation metrics in image analysis. Focusing on biomedical image analysis but with the potential of transfer to other fields, the addressed pitfalls generalize across application domains and are categorized according to a newly created, domain-agnostic taxonomy. To facilitate comprehension, illustrations and specific examples accompany each pitfall. As a structured body of information accessible to researchers of all levels of expertise, this work enhances global comprehension of a key topic in image analysis validation., Comment: Shared first authors: Annika Reinke and Minu D. Tizabi; shared senior authors: Lena Maier-Hein and Paul F. J\"ager. Published in Nature Methods. arXiv admin note: text overlap with arXiv:2206.01653

Dynamic nuclear polarization (DNP) is capable of boosting signals in nuclear magnetic resonance by orders of magnitude by creating out-of-equilibrium nuclear spin polarization. The diffusion of nuclear spin polarization in the vicinity of paramagnetic dopants is a crucial step for DNP and remains yet not well understood. In this Letter, we show that the polarization of the electron spin controls the rate of proton spin diffusion in a DNP sample at 1.2 K and 7 T; at increasingly high electron polarization, spin diffusion vanishes. We rationalize our results using a 2 nucleus - 1 electron model and Lindblad s Master equation, which generalizes preexisting models in the literature and qualitatively accounts for the experimental observed spin diffusion dynamics., Comment: Main text: 6 pages, 3 figures Supplement: 9 pages, 4 figures

Increasing evidence shows that flaws in machine learning (ML) algorithm validation are an underestimated global problem. Particularly in automatic biomedical image analysis, chosen performance metrics often do not reflect the domain interest, thus failing to adequately measure scientific progress and hindering translation of ML techniques into practice. To overcome this, our large international expert consortium created Metrics Reloaded, a comprehensive framework guiding researchers in the problem-aware selection of metrics. Following the convergence of ML methodology across application domains, Metrics Reloaded fosters the convergence of validation methodology. The framework was developed in a multi-stage Delphi process and is based on the novel concept of a problem fingerprint - a structured representation of the given problem that captures all aspects that are relevant for metric selection, from the domain interest to the properties of the target structure(s), data set and algorithm output. Based on the problem fingerprint, users are guided through the process of choosing and applying appropriate validation metrics while being made aware of potential pitfalls. Metrics Reloaded targets image analysis problems that can be interpreted as a classification task at image, object or pixel level, namely image-level classification, object detection, semantic segmentation, and instance segmentation tasks. To improve the user experience, we implemented the framework in the Metrics Reloaded online tool, which also provides a point of access to explore weaknesses, strengths and specific recommendations for the most common validation metrics. The broad applicability of our framework across domains is demonstrated by an instantiation for various biological and medical image analysis use cases., Comment: Shared first authors: Lena Maier-Hein, Annika Reinke. arXiv admin note: substantial text overlap with arXiv:2104.05642 Published in Nature Methods

The Pauli exclusion principle in quantum mechanics has a profound influence on the structure of matter and on interactions between fermions. Almost 30 years ago it was predicted that the Pauli exclusion principle could lead to a suppression of spontaneous emission, and only recently several experiments confirmed this phenomenon. Here we report that this so-called Pauli blockade not only affects incoherent processes but also, more generally, coherently driven systems. It manifests itself as an intriguing sub-Doppler narrowing of a doubly-forbidden transition profile in an optically trapped Fermi gas of $^3\mathrm{He}$. By actively pumping atoms out of the excited state, we break the coherence of the excitation and lift the narrowing effect, confirming the influence of Pauli blockade on the transition profile. This new insight into the interplay between quantum statistics and coherent driving is a promising development for future applications involving fermionic systems., Comment: 36 pages, 8 figures

This paper presents the design and results of the "PEg TRAnsfert Workflow recognition" (PETRAW) challenge whose objective was to develop surgical workflow recognition methods based on one or several modalities, among video, kinematic, and segmentation data, in order to study their added value. The PETRAW challenge provided a data set of 150 peg transfer sequences performed on a virtual simulator. This data set was composed of videos, kinematics, semantic segmentation, and workflow annotations which described the sequences at three different granularity levels: phase, step, and activity. Five tasks were proposed to the participants: three of them were related to the recognition of all granularities with one of the available modalities, while the others addressed the recognition with a combination of modalities. Average application-dependent balanced accuracy (AD-Accuracy) was used as evaluation metric to take unbalanced classes into account and because it is more clinically relevant than a frame-by-frame score. Seven teams participated in at least one task and four of them in all tasks. Best results are obtained with the use of the video and the kinematics data with an AD-Accuracy between 93% and 90% for the four teams who participated in all tasks. The improvement between video/kinematic-based methods and the uni-modality ones was significant for all of the teams. However, the difference in testing execution time between the video/kinematic-based and the kinematic-based methods has to be taken into consideration. Is it relevant to spend 20 to 200 times more computing time for less than 3% of improvement? The PETRAW data set is publicly available at www.synapse.org/PETRAW to encourage further research in surgical workflow recognition., Comment: Challenge report doi.org/10.1016/j.cmpb.2023.107561

Digital technology is everywhere for the benefit of our daily and professional life. It strongly impacts our life and was crucial to maintain professional and social activities during the COVID19 crisis. Similarly, digital technologies are key within biomedical engineering research topics. Innovations have been generated and introduced over the last 40 years, demonstrating how computing and digital technologies have impacted health care. Although the benefits of digital technology are obvious now, we are at the convergence of several issues which makes us aware about social, societal and environmental challenges associated with this technology. In the social domain, digital technologies raise concern about exclusion (financial, geographical, educational, demographical, racial, gender, language, and disabled related exclusion) and physical and mental health. In the societal dimension, digital technologies raise concern about politics and democracy (sovereignty and governance, cognitive filters and citizen's engagement), privacy and security (data acquisition and usage transparency, level of personal approval, and level of anonymization), and economics. In the environmental dimension, digital technologies raise concern about energy consumption and hardware production. This paper introduces and defines these challenges for digital technology in general, as well as when applied to health care. The objective of this paper is to make the research community more aware about the challenges of digital technology and to promote more transparency for innovative and responsible research., Comment: 16 pages, 1 table, 4 figures, 69 references

While the importance of automatic image analysis is continuously increasing, recent meta-research revealed major flaws with respect to algorithm validation. Performance metrics are particularly key for meaningful, objective, and transparent performance assessment and validation of the used automatic algorithms, but relatively little attention has been given to the practical pitfalls when using specific metrics for a given image analysis task. These are typically related to (1) the disregard of inherent metric properties, such as the behaviour in the presence of class imbalance or small target structures, (2) the disregard of inherent data set properties, such as the non-independence of the test cases, and (3) the disregard of the actual biomedical domain interest that the metrics should reflect. This living dynamically document has the purpose to illustrate important limitations of performance metrics commonly applied in the field of image analysis. In this context, it focuses on biomedical image analysis problems that can be phrased as image-level classification, semantic segmentation, instance segmentation, or object detection task. The current version is based on a Delphi process on metrics conducted by an international consortium of image analysis experts from more than 60 institutions worldwide., Comment: Shared first authors: Annika Reinke and Minu D. Tizabi. This is a dynamic paper on limitations of commonly used metrics. It discusses metrics for image-level classification, semantic and instance segmentation, and object detection. For missing use cases, comments or questions, please contact a.reinke@dkfz.de. Substantial contributions to this document will be acknowledged with a co-authorship

The "MIcro-Surgical Anastomose Workflow recognition on training sessions" (MISAW) challenge provided a data set of 27 sequences of micro-surgical anastomosis on artificial blood vessels. This data set was composed of videos, kinematics, and workflow annotations described at three different granularity levels: phase, step, and activity. The participants were given the option to use kinematic data and videos to develop workflow recognition models. Four tasks were proposed to the participants: three of them were related to the recognition of surgical workflow at three different granularity levels, while the last one addressed the recognition of all granularity levels in the same model. One ranking was made for each task. We used the average application-dependent balanced accuracy (AD-Accuracy) as the evaluation metric. This takes unbalanced classes into account and it is more clinically relevant than a frame-by-frame score. Six teams, including a non-competing team, participated in at least one task. All models employed deep learning models, such as CNN or RNN. The best models achieved more than 95% AD-Accuracy for phase recognition, 80% for step recognition, 60% for activity recognition, and 75% for all granularity levels. For high levels of granularity (i.e., phases and steps), the best models had a recognition rate that may be sufficient for applications such as prediction of remaining surgical time or resource management. However, for activities, the recognition rate was still low for applications that can be employed clinically. The MISAW data set is publicly available to encourage further research in surgical workflow recognition. It can be found at www.synapse.org/MISAW, Comment: MICCAI2020 challenge report, 36 pages including 15 for supplementary material (complet results for each participating teams), 17 figures

Recent developments in data science in general and machine learning in particular have transformed the way experts envision the future of surgery. Surgical Data Science (SDS) is a new research field that aims to improve the quality of interventional healthcare through the capture, organization, analysis and modeling of data. While an increasing number of data-driven approaches and clinical applications have been studied in the fields of radiological and clinical data science, translational success stories are still lacking in surgery. In this publication, we shed light on the underlying reasons and provide a roadmap for future advances in the field. Based on an international workshop involving leading researchers in the field of SDS, we review current practice, key achievements and initiatives as well as available standards and tools for a number of topics relevant to the field, namely (1) infrastructure for data acquisition, storage and access in the presence of regulatory constraints, (2) data annotation and sharing and (3) data analytics. We further complement this technical perspective with (4) a review of currently available SDS products and the translational progress from academia and (5) a roadmap for faster clinical translation and exploitation of the full potential of SDS, based on an international multi-round Delphi process.

Modeling and recognition of surgical activities poses an interesting research problem. Although a number of recent works studied automatic recognition of surgical activities, generalizability of these works across different tasks and different datasets remains a challenge. We introduce a modality that is robust to scene variation, and that is able to infer part information such as orientational and relative spatial relationships. The proposed modality is based on spatial temporal graph representations of surgical tools in videos, for surgical activity recognition. To explore its effectiveness, we model and recognize surgical gestures with the proposed modality. We construct spatial graphs connecting the joint pose estimations of surgical tools. Then, we connect each joint to the corresponding joint in the consecutive frames forming inter-frame edges representing the trajectory of the joint over time. We then learn hierarchical spatial temporal graph representations using Spatial Temporal Graph Convolutional Networks (ST-GCN). Our experiments show that learned spatial temporal graph representations perform well in surgical gesture recognition even when used individually. We experiment with the Suturing task of the JIGSAWS dataset where the chance baseline for gesture recognition is 10%. Our results demonstrate 68% average accuracy which suggests a significant improvement. Learned hierarchical spatial temporal graph representations can be used either individually, in cascades or as a complementary modality in surgical activity recognition, therefore provide a benchmark for future studies. To our knowledge, our paper is the first to use spatial temporal graph representations of surgical tools, and pose-based skeleton representations in general, for surgical activity recognition.

The number of biomedical image analysis challenges organized per year is steadily increasing. These international competitions have the purpose of benchmarking algorithms on common data sets, typically to identify the best method for a given problem. Recent research, however, revealed that common practice related to challenge reporting does not allow for adequate interpretation and reproducibility of results. To address the discrepancy between the impact of challenges and the quality (control), the Biomedical I mage Analysis ChallengeS (BIAS) initiative developed a set of recommendations for the reporting of challenges. The BIAS statement aims to improve the transparency of the reporting of a biomedical image analysis challenge regardless of field of application, image modality or task category assessed. This article describes how the BIAS statement was developed and presents a checklist which authors of biomedical image analysis challenges are encouraged to include in their submission when giving a paper on a challenge into review. The purpose of the checklist is to standardize and facilitate the review process and raise interpretability and reproducibility of challenge results by making relevant information explicit., Comment: 2 Appendices - Appendix A: BIAS reporting guideline for biomedical image analysis challenges, Appendix B: Glossary; 2 Supplements - Suppl 1: Form for summarizing information on challenge organization, Suppl 2: Structured description of a challenge design

Objective: A median of 14.4% of patient undergone at least one adverse event during surgery and a third of them are preventable. The occurrence of adverse events forces surgeons to implement corrective strategies and, thus, deviate from the standard surgical process. Therefore, it is clear that the automatic identification of adverse events is a major challenge for patient safety. In this paper, we have proposed a method enabling us to identify such deviations. We have focused on identifying surgeons' deviations from standard surgical processes due to surgical events rather than anatomic specificities. This is particularly challenging, given the high variability in typical surgical procedure workflows. Methods: We have introduced a new approach designed to automatically detect and distinguish surgical process deviations based on multi-dimensional non-linear temporal scaling with a hidden semi-Markov model using manual annotation of surgical processes. The approach was then evaluated using cross-validation. Results: The best results have over 90% accuracy. Recall and precision were superior at 70%. We have provided a detailed analysis of the incorrectly-detected observations. Conclusion: Multi-dimensional non-linear temporal scaling with a hidden semi-Markov model provides promising results for detecting deviations. Our error analysis of the incorrectly-detected observations offers different leads in order to further improve our method. Significance: Our method demonstrated the feasibility of automatically detecting surgical deviations that could be implemented for both skill analysis and developing situation awareness-based computer-assisted surgical systems.

In this paper, we address the open research problem of surgical gesture recognition using motion cues from video data only. We adapt Optical flow ConvNets initially proposed by Simonyan et al.. While Simonyan uses both RGB frames and dense optical flow, we use only dense optical flow representations as input to emphasize the role of motion in surgical gesture recognition, and present it as a robust alternative to kinematic data. We also overcome one of the limitations of Optical flow ConvNets by initializing our model with cross modality pre-training. A large number of promising studies that address surgical gesture recognition highly rely on kinematic data which requires additional recording devices. To our knowledge, this is the first paper that addresses surgical gesture recognition using dense optical flow information only. We achieve competitive results on JIGSAWS dataset, moreover, our model achieves more robust results with less standard deviation, which suggests optical flow information can be used as an alternative to kinematic data for the recognition of surgical gestures.

Surgical data science is a scientific discipline with the objective of improving the quality of interventional healthcare and its value through capturing, organization, analysis, and modeling of data. The goal of the 1st workshop on Surgical Data Science was to bring together researchers working on diverse topics in surgical data science in order to discuss existing challenges, potential standards and new research directions in the field. Inspired by current open space and think tank formats, it was organized in June 2016 in Heidelberg. While the first day of the workshop, which was dominated by interactive sessions, was open to the public, the second day was reserved for a board meeting on which the information gathered on the public day was processed by (1) discussing remaining open issues, (2) deriving a joint definition for surgical data science and (3) proposing potential strategies for advancing the field. This document summarizes the key findings., Comment: 29 pages

International challenges have become the standard for validation of biomedical image analysis methods. Given their scientific impact, it is surprising that a critical analysis of common practices related to the organization of challenges has not yet been performed. In this paper, we present a comprehensive analysis of biomedical image analysis challenges conducted up to now. We demonstrate the importance of challenges and show that the lack of quality control has critical consequences. First, reproducibility and interpretation of the results is often hampered as only a fraction of relevant information is typically provided. Second, the rank of an algorithm is generally not robust to a number of variables such as the test data used for validation, the ranking scheme applied and the observers that make the reference annotations. To overcome these problems, we recommend best practice guidelines and define open research questions to be addressed in the future., Comment: Article published in Nature Communications: https://rdcu.be/bRmNr

Improvements in both theory and frequency metrology of few-electron systems such as hydrogen and helium have enabled increasingly sensitive tests of quantum electrodynamics (QED), as well as ever more accurate determinations of fundamental constants and the size of the nucleus. At the same time advances in cooling and trapping of neutral atoms have revolutionized the development of increasingly accurate atomic clocks. Here, we combine these fields to reach the highest precision on an optical tranistion in the helium atom to date by employing a Bose-Einstein condensate confined in a magic wavelength optical dipole trap. The measured transition accurately connects the ortho- and parastates of helium and constitutes a stringent test of QED theory. In addition we test polarizability calculations and ultracold scattering properties of the helium atom. Finally, our measurement probes the size of the nucleus at a level exceeding the projected accuracy of muonic helium measurements currently being performed in the context of the proton radius puzzle.

Lack of training data hinders automatic recognition and prediction of surgical activities necessary for situation-aware operating rooms. We propose using knowledge transfer to compensate for data deficit and improve prediction. We used two approaches to extract and transfer surgical process knowledge. First, we encoded semantic information about surgical terms using word embedding which boosted learning process. Secondly, we passed knowledge between different clinical datasets of neurosurgical procedures using transfer learning. Transfer learning was shown to be more effective than a simple combination of data, especially for less similar procedures. The combination of two methods provided 22% improvement of activity prediction. We also made several pertinent observations about surgical practices.

Automatic low-level surgical activity recognition is today well-known technical bottleneck for smart and situation-aware assistance for the operating room of the future. Our study sought to discover which sensors and signals could facilitate this recognition. Low-level surgical activity represents semantic information about a surgical procedure that is usually expressed by the following elements: an action verb, surgical instrument, and operated anatomical structure. We hypothesized that activity recognition does not require sensors for all three elements. We conducted a large-scale study using deep learning on semantic data from 154 operations from four different surgeries. The results demonstrated that the instrument and verb encode similar information, meaning only one needs to be tracked, preferably the instrument. The anatomical structure, however, provides some unique cues, and it is thus crucial to recognize it. For all the studied surgeries, a combination of two elements, always including the structure, proved sufficient to confidently recognize the activities. We also found that in the presence of noise, combining the information about the instrument, structure, and historical context produced better results than a simple composition of all three elements. Several relevant observations about surgical practices were also made in this paper. Such findings provide cues for designing a new generation of operating rooms.

This paper introduces Surgical Data Science as an emerging scientific discipline. Key perspectives are based on discussions during an intensive two-day international interactive workshop that brought together leading researchers working in the related field of computer and robot assisted interventions. Our consensus opinion is that increasing access to large amounts of complex data, at scale, throughout the patient care process, complemented by advances in data science and machine learning techniques, has set the stage for a new generation of analytics that will support decision-making and quality improvement in interventional medicine. In this article, we provide a consensus definition for Surgical Data Science, identify associated challenges and opportunities and provide a roadmap for advancing the field., Comment: 10 pages, 2 figures, White paper corresponding to http://www.surgical-data-science.org/workshop2016