SurgT challenge: Benchmark of soft-tissue trackers for robotic surgery

This paper introduces the "SurgT: Surgical Tracking" challenge which was organized in conjunction with the 25th International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI 2022). There were two purposes for the creation of this challenge: (1) the establishment of the first standardized benchmark for the research community to assess soft-tissue trackers; and (2) to encourage the development of unsupervised deep learning methods, given the lack of annotated data in surgery. A dataset of 157 stereo endoscopic videos from 20 clinical cases, along with stereo camera calibration parameters, have been provided. Participants were assigned the task of developing algorithms to track the movement of soft tissues, represented by bounding boxes, in stereo endoscopic videos. At the end of the challenge, the developed methods were assessed on a previously hidden test subset. This assessment uses benchmarking metrics that were purposely developed for this challenge, to verify the efficacy of unsupervised deep learning algorithms in tracking soft-tissue. The metric used for ranking the methods was the Expected Average Overlap (EAO) score, which measures the average overlap between a tracker's and the ground truth bounding boxes. Coming first in the challenge was the deep learning submission by ICVS-2Ai with a superior EAO score of 0.617. This method employs ARFlow to estimate unsupervised dense optical flow from cropped images, using photometric and regularization losses. Second, Jmees with an EAO of 0.583, uses deep learning for surgical tool segmentation on top of a non-deep learning baseline method: CSRT. CSRT by itself scores a similar EAO of 0.563. The results from this challenge show that currently, non-deep learning methods are still competitive. The dataset and benchmarking tool created for this challenge have been made publicly available at https://surgt.grand-challenge.org/. This challenge is expected to contribute to the development of autonomous robotic surgery and other digital surgical technologies.

CholecTriplet2022: Show me a tool and tell me the triplet - An endoscopic vision challenge for surgical action triplet detection

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.

Co-localized augmented human and X-ray observers in collaborative surgical ecosystem

PURPOSE

Image-guided percutaneous interventions are safer alternatives to conventional orthopedic and trauma surgeries. To advance surgical tools in complex bony structures during these procedures with confidence, a large number of images is acquired. While image-guidance is the de facto standard to guarantee acceptable outcome, when these images are presented on monitors far from the surgical site the information content cannot be associated easily with the 3D patient anatomy.

METHODS

In this article, we propose a collaborative augmented reality (AR) surgical ecosystem to jointly co-localize the C-arm X-ray and surgeon viewer. The technical contributions of this work include (1) joint calibration of a visual tracker on a C-arm scanner and its X-ray source via a hand-eye calibration strategy, and (2) inside-out co-localization of human and X-ray observers in shared tracking and augmentation environments using vision-based simultaneous localization and mapping.

RESULTS

We present a thorough evaluation of the hand-eye calibration procedure. Results suggest convergence when using 50 pose pairs or more. The mean translation and rotation errors at convergence are 5.7 mm and [Formula: see text], respectively. Further, user-in-the-loop studies were conducted to estimate the end-to-end target augmentation error. The mean distance between landmarks in real and virtual environment was 10.8 mm.

CONCLUSIONS

The proposed AR solution provides a shared augmented experience between the human and X-ray viewer. The collaborative surgical AR system has the potential to simplify hand-eye coordination for surgeons or intuitively inform C-arm technologists for prospective X-ray view-point planning.

Augmented reality-based feedback for technician-in-the-loop C-arm repositioning

Interventional C-arm imaging is crucial to percutaneous orthopedic procedures as it enables the surgeon to monitor the progress of surgery on the anatomy level. Minimally invasive interventions require repeated acquisition of X-ray images from different anatomical views to verify tool placement. Achieving and reproducing these views often comes at the cost of increased surgical time and radiation. We propose a marker-free ‘technician-in-the-loop’ Augmented Reality (AR) solution for C-arm repositioning. The X-ray technician operating the C-arm interventionally is equipped with a head-mounted display system capable of recording desired C-arm poses in 3D via an integrated infrared sensor. For C-arm repositioning to a target view, the recorded pose is restored as a virtual object and visualized in an AR environment, serving as a perceptual reference for the technician. Our proof-of-principle findings from a simulated trauma surgery indicate that the proposed system can decrease the 2.76 X-ray images required for re-aligning the scanner with an intra-operatively recorded C-arm view down to zero, suggesting substantial reductions of radiation dose. The proposed AR solution is a first step towards facilitating communication between the surgeon and the surgical staff, improving the quality of surgical image acquisition, and enabling context-aware guidance for surgery rooms of the future.

Metal-organic and covalent organic frameworks as single-site catalysts

Heterogeneous single-site catalysts consist of isolated, well-defined, active sites that are spatially separated in a given solid and, ideally, structurally identical. In this review, the potential of metal-organic frameworks (MOFs) and covalent organic frameworks (COFs) as platforms for the development of heterogeneous single-site catalysts is reviewed thoroughly. In the first part of this article, synthetic strategies and progress in the implementation of such sites in these two classes of materials are discussed. Because these solids are excellent playgrounds to allow a better understanding of catalytic functions, we highlight the most important recent advances in the modelling and spectroscopic characterization of single-site catalysts based on these materials. Finally, we discuss the potential of MOFs as materials in which several single-site catalytic functions can be combined within one framework along with their potential as powerful enzyme-mimicking materials. The review is wrapped up with our personal vision on future research directions.

Towards metal-organic framework based field effect chemical sensors: UiO-66-NH2 for nerve agent detection

Kelvin probe monitoring of metal-organic framework coated electrodes is demonstrated as a route for ppb-level detection of alkyl phosphonates.

We present a highly sensitive gas detection approach for the infamous ‘nerve agent’ group of alkyl phosphonate compounds. Signal transduction is achieved by monitoring the work function shift of metal–organic framework UiO-66-NH₂ coated electrodes upon exposure to ppb-level concentrations of a target simulant. Using the Kelvin probe technique, we demonstrate the potential of electrically insulating MOFs for integration in field effect devices such as ChemFETs: a three orders of magnitude improvement over previous work function-based detection of nerve agent simulants. Moreover, the signal is fully reversible both in dry and humid conditions, down to low ppb concentrations. Comprehensive investigation of the interactions that lead towards this high sensitivity points towards a series of confined interactions between the analyte and the pore interior of UiO-66-NH₂.

Travel-acquired infections in Canada: CanTravNet 2011-2012

BACKGROUND

Important gaps remain in our knowledge of the infectious diseases people acquire while travelling and the impact of pathogens imported by Canadian travellers.

OBJECTIVE

To provide a surveillance update of illness in a cohort of returned Canadian travellers and new immigrants.

METHODS

Data on returning Canadian travellers and new immigrants presenting to a CanTravNet site between September 2011 and September 2012 were extracted and analyzed by destination, presenting symptoms, common and emerging infectious diseases and disease severity.

RESULTS

During the study period, 2283 travellers and immigrants presented to a CanTravNet site, 88% (N=2004) of whom were assigned a travel-related diagnosis. Top three destinations for non-immigrant travellers were India (N=132), Mexico (N=103) and Cuba (N=89). Fifty-one cases of malaria were imported by ill returned travellers during the study period, 60% (N=30) of which were Plasmodium falciparum infections. Individuals travelling to visit friends and relatives accounted for 83% of enteric fever cases (15/18) and 41% of malaria cases (21/51). The requirement for inpatient management was over-represented among those with malaria compared to those without malaria (25% versus 2.8%; p<0.0001) and those travelling to visit friends and relatives versus those travelling for other reasons (12.1% versus 2.4%; p<0.0001). Nine new cases of HIV were diagnosed among the cohort, as well as one case of acute hepatitis B. Emerging infections among travellers included hepatitis E virus (N=6), chikungunya fever (N=4) and cutaneous leishmaniasis (N=16). Common chief complaints included gastrointestinal (N=804), dermatologic (N=440) and fever (N=287). Common specific causes of chief complaint of fever in the cohort were malaria (N=47/51 total cases), dengue fever (14/18 total cases), enteric fever (14/17 total cases) and influenza and influenza-like illness (15/21 total cases). Animal bites were the tenth most common diagnosis among tourist travellers.

INTERPRETATION

Our analysis of surveillance data on ill returned Canadian travellers provides a recent update to the spectrum of imported illness among travelling Canadians. Preventable travel-acquired illnesses and injuries in the cohort include malaria, enteric fever, HIV, hepatitis B, hepatitis A, influenza and animal bites. Strategies to improve uptake of preventive interventions such as malaria chemoprophylaxis, immunizations and arthropod/animal avoidance may be warranted.

Is the delay in diagnosis of pulmonary tuberculosis related to exposure to fluoroquinolones or any antibiotic?

BACKGROUND

Delays in diagnosis of tuberculosis (TB) have been associated with previous use of antibiotics, and in particular fluoroquinolones (FQ), for suspected pulmonary infections.

METHODS

We conducted a population-based cohort study with 2232 patients who had active TB between 1997 and 2006 (records obtained from the British Columbia Linked Health Databases). Patients with a record of an initial health care contact preceding the diagnosis of TB were identified for inclusion. Health care delay was defined as the time between initial health care contact and the initiation of anti-tuberculosis medication, and was compared between patients prescribed antibiotics and those not exposed to any antibiotics.

RESULTS

A total of 1544 patients were included. After adjusting for covariates, average health care delay for patients exposed to antibiotics was found to be significantly greater, by a factor of 2.10 (95%CI 1.80-2.44), with a median delay of 41 days in the antibiotic group compared to 14 days in the non-antibiotic group. Sex, age, foreign-born status and socio-economic status were non-significant factors. Health care delay increased with the number of antibiotic courses received, but not with the type of antibiotic.

CONCLUSIONS

Previous treatment with any antibiotic, and not only a FQ, is associated with a delay in TB diagnosis.

Developmental profile of serum nerve growth factor levels in Rett complex

Rett syndrome (RS) is a progressive neurodevelopmental disorder predominant in females, characterised by mental deficiency, stereotyped hand-washing and apraxia. Notwithstanding the recent identification of the MECP2 gene likely involved in the pathogenesis of SR, the neurobiological bases of this syndrome are still largely unknown. Converging evidence shows that the brain levels of nerve growth factor (NGF), a neurotrophin regulating the development and functioning of central cholinergic neurons, are decreased in RS girls. In this study, the serum levels of NGF were measured in classic RS, in the preserved speech variant (PSV) and in normal controls. Overall analysis failed to evidence significant differences among the three groups. However, whereas NGF levels increased significantly with age in controls, the opposite profile was observed in classic RS, with a progressive age-dependent decrease of NGF. In PSV subjects NGF levels remained constant with age. These findings strengthen the hypothesis of NGF involvement in the pathogenesis of RS.

[Salivary testosterone and cognitive ability in children]

There are suggestive data with indicate the link of testosterone levels with specific cognitive abilities in humans. As soon as during intrauterine development, testosterone is supposed to influence to organization of fetal specific brain structures. This influence is permanent and it is reflected in cognitive abilities during prepubetal period. In puberty, the testosterone level rapidly increases mainly in boys and it appears to influence the definitive development of cognitive functions. In this paper, results of the first four years of our logitudinal study are presented. Salivary testosterone levels in children were determined, and their effect on spatial ability was studied. Radioimmunoanalytical method of testosterone determination in saliva was developed, since saliva reflects free fraction of testosterone directly available for uptake by receptors in the central nervous system. The sampling of saliva is non-invasive and unstressful, which is important for relevant evaluation of cognitive performance. One hundred and forty-seven children (78 boys and 69 girls) at the ae of 8 to 12 were examined. The data received from intellectually gifted children attending the School for gifted children in Bratislava (100 measurements) were compared with the data received from age-matched children attending randomly chosen elementary schools (151 measurements). Lower salivary testosterone levels were found in intellectually gifted children of both sexes, and negative relationship between testosterone levels and cognitive abilities in preadolescent children was observed.

Alternate splicing produces a soluble form of the hereditary hemochromatosis protein HFE

HFE is a non-typical MHC class 1-type protein that is mutated in hereditary hemochromatosis. The purpose of this study was to identify possible splice variants of HFE mRNA and investigate the regulation of these isoforms in duodenum and liver of patients with normal and altered iron stores. RT-PCR was performed using HFE specific primers and duodenal RNA obtained from patients with hemochromatosis, iron deficiency, secondary iron overload and normal controls. The reaction products were visualized by Southern blot and identified by DNA sequence analysis. Additional studies were performed on RNA isolated from liver and a range of human tissues. A truncated (soluble) form of HFE protein was identified that lacks the transmembrane domain and occurs as a result of alternative splicing. Soluble HFE was found predominantly in the duodenum, spleen, breast, skin and testicle. In hereditary hemochromatosis full length HFE was the predominant isoform present in the duodenum similar to iron deficiency. Alternate splicing produces soluble HFE that may have a unique function to regulate cellular iron transport.

The value of student-made models as learning aids in physiology

In a new educational scheme introduced in Malta in 1978, university students spend half of the academic year studying and the other half as workers in various departments. During their work phase, students designed and made working models as teaching aids for the study of physiology. The value of these models was assessed on another group of students before they started their physiology course. These students completed a multiple choice questionnaire on three occasions: before and after having seen the models and after they had had them explained. In addition, they completed a questionnaire designed to elicit their views concerning these models. It was found that the models effectively improved knowledge with little staff involvement. The effectiveness of a model as an aid to learning was directly proportional to the degree of its appeal, but inversely proportional to its complexity in terms of stimulating factors. It is suggested that such models could help in teaching, compensating for shortage of staff, and that students' ability to produce teaching models should be wisely exploited.