Detection and removal of dust artifacts in retinal images via sparse-based inpainting

Dust particle artifacts are present in all imaging modalities but have more adverse consequences in medical images like retinal images. They could be mistaken as small lesions, such as microaneurysms. We propose a method for detecting and accurately segmenting dust artifacts in retinal images based on multi-scale template-matching on several input images and an iterative segmentation via an inpainting approach. The inpainting is done through dictionary learning and sparse-based representation. The artifact segmentation is refined by comparing the original image to the initial restoration. On average, 90% of the dust artifacts were detected in the test images, with state-of-theart restoration results. All detected artifacts were accurately segmented and removed. Even the most challenging artifacts located on top of blood vessels were removed. Thus, ensuring the continuity of the retinal structures. The proposed method successfully detects and removes dust artifacts in retinal images, which could be used to avoid false-positive lesion detections or as an image quality criterion. An implementation of the proposed algorithm can be accessed and executed through a Code Ocean compute capsule.The authors acknowledge the financial support from the Centre de Cooperació i Desenvolupament (CCD) at the Universitat Politècnica de Catalunya under project ref. CCD 2019-B004, and from the Universidad Tecnológica de Bolívar. Authors are grateful to Juan Luís Fuentes from the Miguel Servet University Hospital (Zaragoza, Spain) for providing the real images from clinical practice. E. Barrios thanks Minciencias and Sistema General de Regalías (Programa de Becas de Excelencia) for a PhD scholarship. E. Sierra thanks the Universidad Tecnológica de Bolívar for a post-graduate scholarship. Parts of this work were presented at the Pattern Recognition and Tracking XXX - SPIE DCS, 2019 [39]. L. Romero, A. Marrugo, and M.S. Millán thank the funds provided by the Spanish Ministerio de Ciencia e Innovación under the project reference PID2020-114582RB-I00.Peer ReviewedPostprint (published version

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication

Removing dust artifacts in retinal images via dictionary learning and sparse-based inpainting

In the field of ophthalmology, retinal images are essential for the diagnosis of many diseases. These images are acquired with a device called the retinal camera. However, often small dust particles in the sensor produce image artifacts that can be confused with small lesions, such as micro-aneurysms. The digital removal of artifacts can be understood as an inpainting process in which a set of pixels are replaced with a value obtained from the surrounding area. In this paper, we propose a methodology based on the sparse representations and dictionary learning for the removal of artifacts in retinal images. We test our method on real retinal images coming from the clinical setting with actual dust artifacts. We compare our restoration results with a diffusion-based inpainting technique. Encouraging experimental results show that our method can successfully remove the artifacts, while assuring the continuity of the retinal structures, like blood vessels.Peer ReviewedPostprint (published version

Removing dust artifacts in retinal images via dictionary learning and sparse-based inpainting

In the field of ophthalmology, retinal images are essential for the diagnosis of many diseases. These images are acquired with a device called the retinal camera. However, often small dust particles in the sensor produce image artifacts that can be confused with small lesions, such as micro-aneurysms. The digital removal of artifacts can be understood as an inpainting process in which a set of pixels are replaced with a value obtained from the surrounding area. In this paper, we propose a methodology based on the sparse representations and dictionary learning for the removal of artifacts in retinal images. We test our method on real retinal images coming from the clinical setting with actual dust artifacts. We compare our restoration results with a diffusion-based inpainting technique. Encouraging experimental results show that our method can successfully remove the artifacts, while assuring the continuity of the retinal structures, like blood vessels.Peer Reviewe

Robust detection and removal of dust artifacts in retinal images via dictionary learning and sparse-based inpainting

Retinal images are acquired with eye fundus cameras which, like any other camera, can suffer from dust particles attached to the sensor and lens. These particles impede light from reaching the sensor, and therefore they appear as dark spots in the image which can be mistaken as small lesions like microaneurysms. We propose a robust method for detecting dust artifacts from more than one image as input and, for the removal, we propose a sparse-based inpainting technique with dictionary learning. The detection is based on a closing operation to remove small dark features. We compute the difference with the original image to highlight the artifacts and perform a filtering approach with a filter bank of artifact models of different sizes. The candidate artifacts are identified via non-maxima suppression. Because the artifacts do not change position in the images, after processing all input images, the candidate artifacts which are not in the same approximate position in different images are rejected and kept unchanged in the image. The experimental results show that our method can successfully detect and remove artifacts, while ensuring the continuity of retinal structures, such as blood vessels.Peer ReviewedPostprint (published version

Robust detection and removal of dust artifacts in retinal images via dictionary learning and sparse-based inpainting

Retinal images are acquired with eye fundus cameras which, like any other camera, can suffer from dust particles attached to the sensor and lens. These particles impede light from reaching the sensor, and therefore they appear as dark spots in the image which can be mistaken as small lesions like microaneurysms. We propose a robust method for detecting dust artifacts from more than one image as input and, for the removal, we propose a sparse-based inpainting technique with dictionary learning. The detection is based on a closing operation to remove small dark features. We compute the difference with the original image to highlight the artifacts and perform a filtering approach with a filter bank of artifact models of different sizes. The candidate artifacts are identified via non-maxima suppression. Because the artifacts do not change position in the images, after processing all input images, the candidate artifacts which are not in the same approximate position in different images are rejected and kept unchanged in the image. The experimental results show that our method can successfully detect and remove artifacts, while ensuring the continuity of retinal structures, such as blood vessels.Peer Reviewe

Skin color correction via convolutional neural networks in 3D fringe projection profilometry

Fringe Projection Profilometry (FPP) with Digital Light Projector technology is one of the most reliable 3D sensing techniques for biomedical applications. However, besides the fringe pattern images,often a color texture image is needed for an accurate medical documentation. This image may be acquired either by projecting a white image or a black image and relying on ambient light. Color Constancy is essential for a faithful digital record, although the optical properties of biological tissue make color reproducibility challenging. Furthermore, color perception is highly dependent on the illuminant. Here, we describe a deep learning-based method for skin color correction in FPP. We trained a convolutional neural network using a skin tone color palette acquired under different illumination conditions to learn the mapping relationship between the input color image and its counterpart in the sRGB color space. Preliminary experimental results demonstrate the potential for this approach.The authors acknowledge the financial support from the Universidad Technológica de Bolívar (project CI2021P04) and the Centre de Cooperació i Desenvolupament (CCD) at the Universitat Politècnica de Catalunya (project CCD 2020-B014). E. Barrios thanks Minciencias and Sistema General de Regalías (Programa de Becas de Excelencia) for a PhD scholarship.Peer ReviewedPostprint (author's final draft

Surgical site infection after gastrointestinal surgery in children : an international, multicentre, prospective cohort study

Introduction Surgical site infection (SSI) is one of the most common healthcare-associated infections (HAIs). However, there is a lack of data available about SSI in children worldwide, especially from low-income and middle-income countries. This study aimed to estimate the incidence of SSI in children and associations between SSI and morbidity across human development settings. Methods A multicentre, international, prospective, validated cohort study of children aged under 16 years undergoing clean-contaminated, contaminated or dirty gastrointestinal surgery. Any hospital in the world providing paediatric surgery was eligible to contribute data between January and July 2016. The primary outcome was the incidence of SSI by 30 days. Relationships between explanatory variables and SSI were examined using multilevel logistic regression. Countries were stratified into high development, middle development and low development groups using the United Nations Human Development Index (HDI). Results Of 1159 children across 181 hospitals in 51 countries, 523 (45 center dot 1%) children were from high HDI, 397 (34 center dot 2%) from middle HDI and 239 (20 center dot 6%) from low HDI countries. The 30-day SSI rate was 6.3% (33/523) in high HDI, 12 center dot 8% (51/397) in middle HDI and 24 center dot 7% (59/239) in low HDI countries. SSI was associated with higher incidence of 30-day mortality, intervention, organ-space infection and other HAIs, with the highest rates seen in low HDI countries. Median length of stay in patients who had an SSI was longer (7.0 days), compared with 3.0 days in patients who did not have an SSI. Use of laparoscopy was associated with significantly lower SSI rates, even after accounting for HDI. Conclusion The odds of SSI in children is nearly four times greater in low HDI compared with high HDI countries. Policies to reduce SSI should be prioritised as part of the wider global agenda.Peer reviewe