Distance transform and template matching based methods for localization of barcodes and QR codes

Visual codes play an important role in automatic identification, which became an inseparable part of industrial processes. Thanks to the revolution of smartphones and telecommunication, it also becomes more and more popular in everyday life, containing embedded web addresses or other small informative texts. While barcode reading is straightforward in images having optimal parameters (fo cus, illumination, code orientation, and position), localization of code regions is still challenging in many scenarios. Every setup has its own characteristics, there fore many approaches are justifiable. Industrial applications are likely to have more fixed parameters like illumination, camera type and code size, and processing speed and accuracy are the most important requirements. In everyday use, like with smart phone cameras, a wide variety of code types, sizes, noise levels and blurring can be observed, but the processing speed is often not crucial, and the image acquisition process can be repeated in order for successful detection. In this paper, we address this problem with two novel methods for localization of 1D barcodes based on template matching and distance transformation, and a third method for QR codes. Our proposed approaches can simultaneously localize sev eral different types of codes. We compare the effectiveness of the proposed methods with several approaches from the literature using public databases and a large set of synthetic images as a benchmark. The evaluation shows that the proposed methods are efficient, having 84.3% Jaccard accuracy, superior to other approaches. One of the presented approaches is an improvement on our previous work. Our template matching based method is computationally more complex, however, it can be adapted to specific code types producing high accuracy. The other method uses distance transformation, which is fast and gives rough regions of interests that can contain valid visual code candidates

Simple identification tools in FishBase

Simple identification tools for fish species were included in the FishBase information system from its inception. Early tools made use of the relational model and characters like fin ray meristics. Soon pictures and drawings were added as a further help, similar to a field guide. Later came the computerization of existing dichotomous keys, again in combination with pictures and other information, and the ability to restrict possible species by country, area, or taxonomic group. Today, www.FishBase.org offers four different ways to identify species. This paper describes these tools with their advantages and disadvantages, and suggests various options for further development. It explores the possibility of a holistic and integrated computeraided strategy

Edge-Computing Deep Learning-Based Computer Vision Systems

Computer vision has become ubiquitous in today\u27s society, with applications ranging from medical imaging to visual diagnostics to aerial monitoring to self-driving vehicles and many more. Common to many of these applications are visual perception systems which consist of classification, localization, detection, and segmentation components, just to name a few. Recently, the development of deep neural networks (DNN) have led to great advancements in pushing state-of-the-art performance in each of these areas. Unlike traditional computer vision algorithms, DNNs have the ability to generalize features previously hand-crafted by engineers specific to the application; this assumption models the human visual system\u27s ability to generalize its surroundings. Moreover, convolutional neural networks (CNN) have been shown to not only match, but exceed performance of traditional computer vision algorithms as the filters of the network are able to learn important features present in the data. In this research we aim to develop numerous applications including visual warehouse diagnostics and shipping yard managements systems, aerial monitoring and tracking from the perspective of the drone, perception system model for an autonomous vehicle, and vehicle re-identification for surveillance and security. The deep learning models developed for each application attempt to match or exceed state-of-the-art performance in both accuracy and inference time; however, this is typically a trade-off when designing a network where one or the other can be maximized. We investigate numerous object-detection architectures including Faster R-CNN, SSD, YOLO, and a few other variations in an attempt to determine the best architecture for each application. We constrain performance metrics to only investigate inference times rather than training times as none of the optimizations performed in this research have any effect on training time. Further, we will also investigate re-identification of vehicles as a separate application add-on to the object-detection pipeline. Re-identification will allow for a more robust representation of the data while leveraging techniques for security and surveillance. We also investigate comparisons between architectures that could possibly lead to the development of new architectures with the ability to not only perform inference relatively quickly (or in close-to real-time), but also match the state-of-the-art in accuracy performance. New architecture development, however, depends on the application and its requirements; some applications need to run on edge-computing (EC) devices, while others have slightly larger inference windows which allow for cloud computing with powerful accelerators

DNA barcoding as a tool to explore elasmobranch diversity in environmental DNA off the Banc d´Arguin (Mauritania)

Sharks and rays are the most threatened group of marine vertebrates. Extinction risk is highest for species in tropical and subtropical areas, often associated with developing nations that generally lack baseline data on species diversity. Although considered a regional elasmbranch hotspot, species diversity in the Banc d’Arguin National Park (PNBA) in Mauritania has not been characterized. Here, a first description of species diversity is provided based on a combination of approaches. DNA barcoding was used to build a regional genetic reference database of species sampled at local processing and landing sites. Two potentially new species (genus Gymnura and Torpedo) were found and possible new lineages for Sphyrna lewini and Aetomylaeus bovinus were uncovered, however, results should be observed with caution and are pending further confirmation. Mustelus punctulatus and Hypanus rudis were confirmed from Mauritania for the first time, extending their known distribution range. Metabarcoding was used to explore species diversity in eDNA samples from the PNBA. Results confirmed the presence of 29 different species, 12 sharks and 17 rays of which 14 species had previously never been reported from the PNBA in the literature. Notably, Mustelus punctulatus was found in 77% of the eDNA samples, while the only locally reported smoothhound, M. mustelus, was absent in all samples. Sphyrna lewini, a species previously reported, was absent from all eDNA samples, however its presence was visually confirmed. Putative new Gymnura and Torpedo species were found throughout various eDNA samples. A total of 66.6% of shark and ray species in the PNBA are threatened with extinction (including S. lewini). Considering the high fishing pressure sharks and rays are exposed to, these results emphasize the importance of taxonomic identification for individual species management and provide a baseline to inform future studies and shark and ray specific conservation measures in the PNBA.Os tubarões e as raias são o grupo de vertebrados marinhos mais ameaçado, principalmente devido a um aumento contínuo do esforço de pesca ao longo das últimas décadas. Os peixes cartilagíneos são inerentemente mais susceptíveis à pressão da pesca devido às características da história de vida que geralmente incluem crescimento lento, maturação tardia e baixa fecundidade. Actualmente, mais de um terço das espécies são de grande preocupação em termos de conservação. O risco de extinção é maior para espécies em áreas tropicais e subtropicais, frequentemente associadas a nações em desenvolvimento que geralmente carecem de dados de base sobre diversidade de espécies e capacidade de monitorização adequada. Um desses países é a Mauritânia, localizada na África subsaariana ocidental, que alberga a maior área marinha protegida da África ocidental, o Parc National du Banc d'Arguin (PNBA), criado em 1976. Os tubarões e as raias eram fortemente explorados na área antes de 2003, quando a gestão do PNBA e a população de pescadores indígenas, aos quais foram concedidos direitos exclusivos de pesca em 2000, acordaram numa moratória sobre quase toda a pesca dirigida ao tubarão e às raias. No entanto, a pressão da pesca de tubarões e raias não parece ter diminuído e o grupo parece representar entre 35% e 45% dos desembarques no PNBA. Embora tenha sido considerado um hotspot regional de tubarões e arraias, a diversidade de espécies no PNBA não foi caracterizada anteriormente. Aqui, a taxonomia das espécies locais é revista e é fornecida uma descrição detalhada da diversidade de espécies com base numa combinação de abordagens. A codificação de barras de ADN foi utilizada para construir uma base de dados de referência de sequência genética 12S específica de espécies amostradas em locais de processamento e aterragem de tubarões e raias locais entre Outubro de 2020 e Abril de 2021. Os genes COI e NADH2 foram utilizados para confirmar algumas identidades ambíguas de espécies que não puderam ser determinadas com confiança apenas através do 12S. Um total de 28 espécies foram codificadas com códigos de barras, das quais 12 eram tubarões e 16 eram raias. 14 espécies forneceram códigos de barras totalmente novos 12S à base de dados global e quatro espécies forneceram novos códigos de barras COI. Duas espécies potencialmente novas no género Gymnura e Torpedo, aqui referidas como Gymnura sp. e Torpedo sp., foram encontradas e preliminarmente corroboradas com base em resultados genéticos, bem como em diferenças morfológicas com outras espécies descritas dentro do seu género. Possíveis novas linhagens nas espécies Sphyrna lewini e Aetomylaeus bovinus foram descobertas, mas devem ser observadas com cautela e estão pendentes de confirmação genética e morfológica adicional. Foi encontrada uma Rhinobatos rhinobatos de forma anormal, que foi compatível com a espécie com base em sequências 12S, levando à conclusão preliminar de que o focinho arredondado dos espécimes é uma deformação morfológica. Da mesma forma, R. rhinobatos com padrões de coloração distintos semelhantes a R. irvinei foram atribuídos à espécie anterior com base em combinações de sequências 12S. No entanto, a confirmação para ambas está pendente de análise genética adicional, dado que as sequências 12S aqui codificadas mostram geralmente taxas de divergência mais baixas do que outros genes. Mustelus punctulatus e Hypanus rudis foram confirmados na Mauritânia pela primeira vez, estendendo a sua conhecida área de distribuição a sul do Sahara Ocidental e a norte da Gâmbia, respectivamente. Uma espécie do género Fontitrygon não pôde ser resolvida com confiança ao nível da espécie e foi tratada como F. margarita/margaritella. No total, 19 das 28 espécies (20 se incluir F. margarita) são colocadas numa das três categorias de ameaça determinadas pela Lista Vermelha da IUCN, com seis espécies avaliadas como Criticamente Ameaçadas, cinco como Ameaçadas e oito (ou nove) como Vulneráveis. As espécies ameaçadas de extinção constituem 68% (ou 71%) das espécies de código de barras neste estudo. Além disso, foi utilizado um ensaio de metabarcodificação específica de tubarões e raias para confirmar a presença de espécies no PNBA. Um total de 29 espécies, 12 tubarões e 17 espécies de raias, estiveram presentes em amostras de eDNA colhidas em locais espalhados pelas áreas norte, centro e sul do PNBA, incluindo uma espécie não identificada de Myliobatis, presumivelmente M. aquila. Uma única amostra colhida fora dos limites do PNBA detectou 12 espécies, contudo não mostrou diversidade adicional de espécies. Foram também recolhidas amostras de DNA ambiental em poços de salga em locais de processamento de tubarões e arraias para avaliar a utilidade do método na detecção de algumas espécies menos comuns e corroborar a sua utilidade como possível ferramenta de monitorização futura em locais de processamento. Os resultados de metabarcodificação confirmaram a presença de 29 espécies diferentes no PNBA, das quais 12 são tubarões e 17 são raias, e das quais 14 espécies nunca tinham sido anteriormente registadas do PNBA na literatura, algumas das quais são tubarões de maiores dimensões, pelágicos ou de águas mais profundas, cuja presença no PNBA é presumivelmente transitória. Outras espécies incluem arraias da família Dasyatidae que são frequentemente reportadas apenas a nível familiar ou de género e que, por conseguinte, podem ter estado ausentes dos registos de desembarque anteriores. Notavelmente, Mustelus punctulatus foi encontrado em 77% das amostras de eDNA do PNBA, enquanto a única espécie Mustelus reportada localmente, M. mustelus, estava ausente em todas as amostras. Squalus acanthias, uma espécie comum em regiões de águas temperadas e frias, foi detectada em 69% das amostras, mas a sua presença ainda não foi confirmada visualmente. Sphyrna lewini, uma espécie comumente capturada no PNBA, esteve ausente em todas as amostras de eDNA, mas a sua presença foi confirmada visualmente. As putativas novas espécies de Gymnura e Torpedo foram ambas encontradas em várias amostras de eDNA. De um total de 29 espécies positivamente identificadas a partir de amostras recolhidas dentro dos limites do PNBA, seis espécies estão Criticamente em Perigo (20,7%) se assumirmos a presença de M. aquila. Cinco espécies estão em Perigo (17,2%) e oito são Vulneráveis (27,6%) na Lista Vermelha da IUCN. As espécies listadas como ameaçadas de extinção no PNBA ascendem portanto a 65,5% e incluem as sete espécies mais abundantes em termos de abundância de leitura. Ao incluir S. lewini, o número de espécies de tubarões e raias ameaçadas no PNBA aumenta para 66,6%. Em amostras de eDNA dos poços de salga, um total de 26 espécies foram detectadas em apenas duas amostras, incluindo seis espécies não detectadas em amostras ambientais, nomeadamente Galeocerdo cuvier, S. lewini, Sphyrna zygaena, Sphyrna mokarran, Torpedo marmorata e Pseudotriakis microdon e três espécies que não foram observadas in situ (G. cuvier, T. marmorata e P. microdon). Apenas uma espécie confirmada in situ não foi detectada em amostras de eDNA (Raja parva). Este estudo representa tanto o primeiro exaustivo esforço regional de codificação de barras como o primeiro levantamento de elasmobrânquios de eDNA na África Ocidental. É também o primeiro a caracterizar a diversidade de espécies de tubarões e raias no PNBA, utilizando ferramentas de levantamento molecular. Considerando que as espécies de alta pressão de pesca estão expostas no PNBA e o precário estado de conservação de uma elevada proporção de espécies locais, estes resultados enfatizam a importância da identificação taxonómica para a gestão individual das espécies e fornecem uma importante base de referência para futuros estudos e medidas de conservação específicas de tubarões e raias no PNBA

Chapter Ten - Informing marine spatial planning decisions with environmental DNA

Marine management areas provide a key tool for efforts towards sustainable development, reconciling socio-economic goals with those for biodiversity conservation. Decisions about where and when to establish spatial management areas in the oceans are currently hampered by the uncertainties of incomplete, or overly general, information about biodiversity. The analysis of environmental DNA (eDNA) provides a potentially powerful tool to overcome this lack of data in the future. Here we present directions to develop robust approaches to integrate eDNA and spatial planning processes, aiming to provide guidance to underpin tool development. The potential of eDNA use in conservation is widely recognised, although direct applications almost exclusively focus on detection of invasive or threatened species and not spatial management decisions. The implementation of broader interaction between the fields of conservation science and eDNA analysis could create substantial benefits to biodiversity conservation and management. In particular, eDNA analysis can provide information on biodiversity over spatial-temporal scales that are currently prohibitive in spatial planning studies. Here, we provide an overview of how eDNA is currently used in conservation practice, in addition to understanding its limitations and benefits within the context of spatial planning. With the goal to harness rapid technological developments in both molecular and conservation sciences, we provide a horizon scan of the future of eDNA analysis and its application to inform biodiversity conservation in a rapidly changing world

Integration of multiple geospatial applications and intelligence for responding to COVID-19 in Ghana

Objective: We describe the use of integrated geospatial applications for the provision of access to timely and accurate data on samples, visualisation of Spatio-temporal patterns of cases and effective communication between field sample collectors, testing laboratories, Regional Health directors and Government Decision Makers.Design: This study describes how an integrated geospatial platform based on case location and intelligence was developed and used for effective COVID-19 response during the initial stages of COVID-19 in Ghana.Data Source: Collector for ArcGIS, ArcGIS Survey123Main outcome measure: successful development and deployment of integrated geospatial applications and analytics.                                                              Results: The Collector for ArcGIS app was customised to collect COVID-19 positive cases location information. Survey 123 was introduced as a COVID-19 contact tracing application to digitise the case-based forms and provide real-time results from the laboratories to GHS and other stakeholders. The laboratory backend allowed the testing laboratories access to specific information about each patient (sample) collected by the fieldworkers. The regional supervisors’ backend web application provided accessing test results for confidentiality and timely communication of results.Conclusion: Geospatial platforms were successfully established in Ghana to provide timely results to Regional Health Directors and Government decision-makers. This helped to improve the timeliness of response and contact tracing at the district level

2D-barcode for mobile devices

2D-barcodes were designed to carry significantly more data than its 1D counterpart. These codes are often used in industrial information tagging applications where high data capacity, mobility, and data robustness are required. Wireless mobile devices such as camera phones and Portable Digital Assistants (PDAs) have evolved from just a mobile voice communication device to what is now a mobile multimedia computing platform. Recent integration of these two mobile technologies has sparked some interesting applications where 2D-barcodes work as visual tags and/or information source and camera phones performs image processing tasks on the device itself. One of such applications is hyperlink establishment. The 2D symbol captured by a camera phone is decoded by the software installed in the phone. Then the web site indicated by the data encoded in a symbol is automatically accessed and shown in the display of the camera phone. Nonetheless, this new mobile applications area is still at its infancy. Each proposed mobile 2D-barcode application has its own choice of code, but no standard exists nor is there any study done on what are the criteria for setting a standard 2D-barcode for mobile phones. This study intends to address this void. The first phase of the study is qualitative examination. In order to select a best standard 2D-barcode, firstly, features desirable for a standard 2D-barcode that is optimized for the mobile phone platform are identified. The second step is to establish the criteria based on the features identified. These features are based on the operating limitations and attributes of camera phones in general use today. All published and accessible 2D-barcodes are thoroughly examined in terms of criteria set for the selection of a best 2D-barcode for camera phone applications. In the second phase, the 2D-barcodes that have higher potential to be chosen as a standard code are experimentally examined against the three criteria: light condition, distance, whether or not a 2D-barcode supports VGA resolution. Each sample 2D-barcode is captured by a camera phone with VGA resolution and the outcome is tested using an image analysis tool written in the scientific language called MATLAB. The outcome of this study is the selection of the most suitable 2D-barcode for applications where mobile devices such as camera phones are utilized

Framing Cutting-Edge Integrative Deep-Sea Biodiversity Monitoring via Environmental DNA and Optoacoustic Augmented Infrastructures

Deep-sea ecosystems are reservoirs of biodiversity that are largely unexplored, but their exploration and biodiscovery are becoming a reality thanks to biotechnological advances (e.g., omics technologies) and their integration in an expanding network of marine infrastructures for the exploration of the seas, such as cabled observatories. While still in its infancy, the application of environmental DNA (eDNA) metabarcoding approaches is revolutionizing marine biodiversity monitoring capability. Indeed, the analysis of eDNA in conjunction with the collection of multidisciplinary optoacoustic and environmental data, can provide a more comprehensive monitoring of deep-sea biodiversity. Here, we describe the potential for acquiring eDNA as a core component for the expanding ecological monitoring capabilities through cabled observatories and their docked Internet Operated Vehicles (IOVs), such as crawlers. Furthermore, we provide a critical overview of four areas of development: (i) Integrating eDNA with optoacoustic imaging; (ii) Development of eDNA repositories and cross-linking with other biodiversity databases; (iii) Artificial Intelligence for eDNA analyses and integration with imaging data; and (iv) Benefits of eDNA augmented observatories for the conservation and sustainable management of deep-sea biodiversity. Finally, we discuss the technical limitations and recommendations for future eDNA monitoring of the deep-sea. It is hoped that this review will frame the future direction of an exciting journey of biodiscovery in remote and yet vulnerable areas of our planet, with the overall aim to understand deep-sea biodiversity and hence manage and protect vital marine resources