scholarly journals Tracking bacteria at high density with FAST, the Feature-Assisted Segmenter/Tracker

2021 ◽  
Author(s):  
Oliver J Meacock ◽  
William M Durham
Keyword(s):  
Modular Design ◽  
Imaging Techniques ◽  
Ease Of Use ◽  
Tracking Errors ◽  
User Input ◽  
Complex Processes ◽  
Cell Position ◽  
Cell Trajectories ◽  
Distinguishing Features ◽  
Naive Approach

Most bacteria live attached to surfaces in densely-packed communities. While new experimental and imaging techniques are beginning to provide a window on the complex processes that play out in these communities, resolving the behaviour of individual cells through time and space remains a major challenge. Although a number of different software solutions have been developed to track microorganisms, these approaches typically rely on a large number of user-defined parameters that must be carefully tuned to effectively track cells. Testing a given parameter combination can take hours to days depending on the size of the dataset, making iterative optimisation impractical. To overcome these limitations, we have developed FAST, the Feature-Assisted Segmenter/Tracker, which uses unsupervised machine learning to optimise tracking while maintaining ease of use. Our approach, rooted in information theory, largely eliminates the need for users to iteratively adjust parameters manually and make qualitative assessments of the resulting cell trajectories. Instead, FAST measures multiple distinguishing "features" for each cell and then autonomously quantifies the amount of unique information each feature provides. We then use these measurements to determine how data from each feature should be combined to minimize tracking errors. Comparing our algorithm with a naïve approach that uses cell position alone revealed that FAST produced 4 to 10 times fewer tracking errors. The modular design of FAST combines our novel tracking method with tools for segmentation, extensive data visualisation, lineage assignment, and manual track correction. It is also highly extensible, allowing users to extract custom information from images and seamlessly integrate it into downstream analyses. FAST therefore enables high-throughput, data-rich analyses with minimal user input. It has been released for use in either Matlab or as a compiled stand-alone application, and is available at https://bit.ly/3vovDHn, along with extensive tutorials and detailed documentation.

scholarly journals Diffuse retro-reflective imaging for improved video tracking of mosquitoes at human baited bednets

2020 ◽  
Vol 7 (5) ◽  
pp. 191951 ◽  
Author(s):  
Vitaly Voloshin ◽  
Christian Kröner ◽  
Chandrabhan Seniya ◽  
Gregory P. D. Murray ◽  
Amy Guy ◽  
...  
Keyword(s):  
Large Scale ◽  
Imaging Techniques ◽  
Field Studies ◽  
Noise Removal ◽  
Optical Signal ◽  
Video Tracking ◽  
Ease Of Use ◽  
Model Systems ◽  
Mosquito Behaviour ◽  
Set Up

Robust imaging techniques for tracking insects have been essential tools in numerous laboratory and field studies on pests, beneficial insects and model systems. Recent innovations in optical imaging systems and associated signal processing have enabled detailed characterization of nocturnal mosquito behaviour around bednets and improvements in bednet design, a global essential for protecting populations against malaria. Nonetheless, there remain challenges around ease of use for large-scale in situ recordings and extracting data reliably in the critical areas of the bednet where the optical signal is attenuated. Here, we introduce a retro-reflective screen at the back of the measurement volume, which can simultaneously provide diffuse illumination, and remove optical alignment issues while requiring only one-sided access to the measurement space. The illumination becomes significantly more uniform, although noise removal algorithms are needed to reduce the effects of shot noise, particularly across low-intensity bednet regions. By systematically introducing mosquitoes in front of and behind the bednet in laboratory experiments, we are able to demonstrate robust tracking in these challenging areas. Overall, the retro-reflective imaging set-up delivers mosquito segmentation rates in excess of 90% compared to less than 70% with backlit systems.

scholarly journals Diffuse retro-reflective imaging for improved video tracking of mosquitoes at human baited bednets

2019 ◽  
Author(s):  
Vitaly Voloshin ◽  
Christian Kröner ◽  
Chandrabhan Seniya ◽  
Gregory P. D. Murray ◽  
Amy Guy ◽  
...  
Keyword(s):  
Large Scale ◽  
Imaging Techniques ◽  
Field Studies ◽  
Noise Removal ◽  
Optical Signal ◽  
Video Tracking ◽  
Ease Of Use ◽  
Model Systems ◽  
Diffuse Illumination ◽  
Mosquito Behaviour

AbstractRobust imaging techniques for tracking insects have been essential tools in numerous laboratory and field studies on pests, beneficial insects and model systems. Recent innovations in optical imaging systems and associated signal processing have enabled detailed characterisation of nocturnal mosquito behaviour around bednets and improvements in bednet design, a global essential for protecting populations against malaria. Nonetheless, there remain challenges around ease of use for large scale in situ recordings and extracting data reliably in the critical areas of the bednet where the optical signal is attenuated. Here we introduce a retro-reflective screen at the back of the measurement volume, which can simultaneously provide diffuse illumination, and remove optical alignment issues whilst requiring only one-sided access to the measurement space. The illumination becomes significantly more uniform, although, noise removal algorithms are needed to reduce the effects of shot noise particularly across low intensity bednet regions. By systematically introducing mosquitoes in front and behind the bednet in lab experiments we are able to demonstrate robust tracking in these challenging areas. Overall, the retro-reflective imaging setup delivers mosquito segmentation rates in excess of 90% compared to less than 70% with back-lit systems.

EEG-based brain imaging techniques in psychiatry

2009 ◽  
Vol 21 (S2) ◽  
pp. 65-66
Author(s):  
Umberto Volpe
Keyword(s):  
Brain Imaging ◽  
Imaging Techniques ◽  
High Sensitivity ◽  
Brain Regions ◽  
Psychiatric Illnesses ◽  
Complex Processes ◽  
Imaging Tool ◽  
Complex Interactions ◽  
The Central Nervous System

Abstract:Electroencephalography has probably represented the first modern and scientifically sound attempt to functionally explore the in vivo activity of the human brain and it has, since ever, attracted attention of psychiatrists, from both the clinical and the research viewpoint.Probably due to the limitations implied by their traditional low spatial resolution, the use of psychophysiological techniques in psychiatry has been not continuous over the last century; however, the availability of newer EEG-based brain imaging techniques has recently renovated some interest (1)). Furthermore, recent theories proposed that psychopathology may result from the failure to integrate the activity of different areas involved in cognitive processes, rather than from the impairment of one or more brain areas (2)); within this view, a reliable brain imaging tool should be able to explore the dynamics of complex interactions among brain regions, with high sensitivity to the subtle deviation in complex processes that last fractions of seconds; psychophysiological techniques, indeed, offer the possibility to explore the functional correlates of major psychiatric illnesses, as well as to understand of the effects of psychotropic drugs on the central nervous system, with incomparable time resolution. Finally, the recent technical possibility to combine different brain imaging approaches has further fostered a renovated enthusiasm to ward the use of EEG-based techniques in psychiatry.This contribution will provide an historical overview of the EEG-based brain imaging techniques and an update on some recent advances concerning the use of such techniques within the psychiatric field. Finally, some examples of psychophysiological and ''multimodal'' imaging investigations in subjects with different psychiatric conditions will be provided.

scholarly journals Neuroimaging findings in MOGAD -- MRI and OCT

2021 ◽  
Author(s):  
Frederik Bartels ◽  
Angelo Lu ◽  
Frederike Oertel ◽  
Carsten Finke ◽  
Friedemann Paul ◽  
...  
Keyword(s):  
In Vivo Imaging ◽  
Imaging Techniques ◽  
Myelin Oligodendrocyte Glycoprotein ◽  
Neuromyelitis Optica Spectrum Disorder ◽  
Resonance Imaging ◽  
Future Studies ◽  
Imaging Characteristics ◽  
Distinguishing Features ◽  
The Brain

Summary Myelin oligodendrocyte glycoprotein antibody associated disorders (MOGAD) are rare in both children and adults, and have been recently suggested to be an autoimmune neuroinflammatory group of disorders that are different from aquaporin-4 autoantibody associated neuromyelitis optica spectrum disorder and from classic multiple sclerosis. In vivo imaging of the MOGAD patient central nervous system has shown some distinguishing features when evaluating magnetic resonance imaging of the brain, spinal cord, optic nerves, as well as retinal imaging using optical coherence tomography. In this review, we discuss key clinical and imaging characteristics of paediatric and adult MOGAD. We describe how these imaging techniques may be used to study this group of disorders and discuss how these imaging methods have led to recent insights for consideration in future studies.

scholarly journals Tools for attracting buyers to e-commerce resources

2019 ◽  
pp. 6-15
Author(s):  
M. Trofimchuk ◽  
O. Bondar ◽  
V. Novikova ◽  
O. Savchuk ◽  
O. Tkachenko
Keyword(s):  
Customer Service ◽  
Social Networking Sites ◽  
Geographic Location ◽  
Ease Of Use ◽  
Electronic Market ◽  
Social Commerce ◽  
Complex Processes ◽  
Keywords Internet ◽  
Communication Devices ◽  
Internet Shop

The Internet provides access to state-of-the-art tools for attracting, securing and organizing customer service with widely available means of communication, regardless of their geographic location or on-the-go journeys. The study of the electronic market, approaches and tools used in e-commerce is devoted to a significant number of scientific robots. Among them are the study of factors that facilitate the expansion of access to e-commerce not only in the world, but also outside cities within countries. Considerable attention in researches is paid to the growing popularity of social networking sites, which leads to the development of a new type of e-commerce - social commerce. Various strategies for reaching the maximum number of communication channels with retail clients are considered. The article examines the current state and analyzes the main tendencies of the development of the electronic market of Ukraine for the continuous development of the possibilities of both communication devices themselves and various e-commerce systems available on the network. Analysis of statistical data has shown that e-commerce tools in commercial transactions increase confidence in decision-making and enable market participants to be more demanding in their ease of use. The features of various ways of attracting consumers to places of sale, factors of the further growth of e-commerce as one of the perspective spheres of investment are explored. As a result of complex processes taking place in the electronic market, an e-business that has digitized and, accordingly, more efficient processes, is more likely to reduce costs and potentially more profits. The process of improving e-business in turn affects the trends of electronic information globalization. Keywords: Internet-shop, site, electronic commerce, electronic market, Internet, press-aggregators, organic search, social commerce.

scholarly journals Imaging Techniques Used for Wound Healing Assessment: A Systematic Review Part 1 Chronic Wounds

2021 ◽  
Vol 2 (4) ◽  
pp. 194-214
Author(s):  
Poh Tan ◽  
Joanne Lim ◽  
Naiem Moiemen
Keyword(s):  
Wound Healing ◽  
Chronic Wounds ◽  
Imaging Techniques ◽  
Objective Assessment ◽  
Ease Of Use ◽  
Secondary Outcome ◽  
Two Dimensional ◽  
Validity And Reliability ◽  
Measuring Device ◽  
Mesh Terms

Background: chronic wounds are complex to manage and require an objective assessment for diagnosis and prognosis purposes. Therefore, this article aims to provide an overview of available noninvasive imaging techniques for chronic wound healing described in the literature. Methods: a systematic literature review using electronic databases was performed with appropriate “Mesh” terms. The primary outcome was the validity and reliability of the instrument, whilst the secondary outcome was its feasibility, such as speed of assessment, ease of use and cost of the tool. All studies underwent quality assessment of diagnostic accuracy studies (QUADAS) to ensure the quality of the data. Results: 44 articles were identified evaluating six wound assessment modalities. Most studies (n = 9) reported on a two-dimensional device with a mean error ranging from 1.9–5.1% and an inter/intra rater correlation over 0.9 with a high ICC (>95%). The average QUADAS score was 13, with the lowest being 9 and the highest being 14. Conclusion: this review collectively evaluates objective, reliable, quantitative, and innovative tools to assess wound healing objectively. The most superior wound measuring device was two dimensional. However, hyperspectral imaging had strong potential but required further development in its technology and future clinic validation studies.

scholarly journals BIDS Apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods

2016 ◽  
Author(s):  
Krzysztof J. Gorgolewski ◽  
Fidel Alfaro-Almagro ◽  
Tibor Auer ◽  
Pierre Bellec ◽  
Mihai Capotă ◽  
...  
Keyword(s):  
Data Analysis ◽  
High Performance ◽  
Ease Of Use ◽  
Imaging Data ◽  
User Input ◽  
Analysis Methods ◽  
Wide Range ◽  
Neuroimaging Data ◽  
Magnetic Resonance Imaging Mri ◽  
Data Analysis Methods

AbstractThe rate of progress in human neurosciences is limited by the inability to easily apply a wide range of analysis methods to the plethora of different datasets acquired in labs around the world. In this work, we introduce a framework for creating, testing, versioning and archiving portable applications for analyzing neuroimaging data organized and described in compliance with the Brain Imaging Data Structure (BIDS). The portability of these applications (BIDS Apps) is achieved by using container technologies that encapsulate all binary and other dependencies in one convenient package. BIDS Apps run on all three major operating systems with no need for complex setup and configuration and thanks to the comprehensiveness richness of the BIDS standard they require little manual user input. Previous containerized data processing solutions were limited to single user environments and not compatible with most multi-tenant High Performance Computing systems. BIDS Apps overcome this limitation by taking advantage of the Singularity container technology. As a proof of concept, this work is accompanied by 22 ready to use BIDS Apps, packaging a diverse set of commonly used neuroimaging algorithms.Author SummaryMagnetic Resonance Imaging (MRI) is a non-invasive way to measure human brain structure and activity that has been used for over 25 years. There are thousands MRI studies performed every year generating a substantial amount of data. At the same time, many new data analysis methods are being developed every year. The potential of using new analysis methods on the variety of existing and newly acquired data is hindered by difficulties in software deployment and lack of support for standardized input data. Here we propose to use container technology to make deployment of a wide range of data analysis techniques easy. In addition, we adapt the existing data analysis tools to interface with data organized in a standardized way. We hope that this approach will enable researchers to access a wider range of methods when analyzing their data which will lead to accelerated progress in human neuroscience.

scholarly journals Experimental and Clinical Approaches to Recovery after Stroke

2015 ◽  
Vol 10 (01) ◽  
pp. 65
Author(s):  
Michael Brainin ◽  
Natan Bornstein ◽  
◽  
Keyword(s):  
Stroke Risk ◽  
Imaging Techniques ◽  
Local Treatment ◽  
Optimal Recovery ◽  
Stroke Recovery ◽  
Supporting Evidence ◽  
Non Invasive ◽  
Complex Processes ◽  
Positron Emission ◽  
Functional Areas

The development of effective treatments that aid recovery after stroke has been hampered in recent decades by a lack of knowledge regarding stroke complexity and the processes involved in neurological repair. Many stroke treatments tested so far have been monomodal, targeting only one neurobiological process whereas multimodal treatments are more likely to address the complex processes of stroke recovery. Understanding of stroke recovery, however, is increasing using imaging techniques, especially positron emission tomography (PET). This reveals features such as the tissue at risk in the peri-infarct area, which can be functionally restored if treatment is initiated rapidly. Understanding of stroke risk is also improving with the use of biomarkers. A promising approach to stroke therapy is non-invasive brain stimulation (NIBS), which can precisely target specific functional areas of the cortex. Clinical studies indicate that NIBS provides improvements in motor functions and aphasia but more supporting evidence is needed. When treating stroke it is critically important to take account of co-morbidities, such as diabetes and hypertension, since these have profound effects on outcomes. The provision of adequate rehabilitation soon after stroke is critical for optimal recovery and should include drug therapy. Such interventions at local treatment centres, however, are often under-resourced. Current developments are leading to a better understanding of pathophysiology and improved awareness of risks and treatments should, in future, also improve rehabilitation and hence benefit outcomes following a stroke.

scholarly journals crossword: A data-driven simulation language for the design of genetic-mapping experiments and breeding strategies

2018 ◽  
Author(s):  
Korani Walid ◽  
Justin N Vaughn
Keyword(s):  
Ease Of Use ◽  
Data Driven ◽  
Domain Specific Language ◽  
Breeding Strategies ◽  
Graphical Interface ◽  
Breeding Programs ◽  
User Input ◽  
Domain Specific ◽  
Simulation Language ◽  
Crop Genetics

AbstractThe simulation of genetic systems can save time and resources by optimizing the logistics of an experiment. Current tools are difficult to use by those unfamiliar with programming, and these tools rarely address the actual genetic structure of the population under study. Here, we introduce crossword, which utilizes the widely available results of re-sequencing and genomics data to create more realistic simulations and to simplify user input. The software was written in R, making installation and implementation straightforward. Because crossword is a domain-specific language, it allows complex and unique simulations to be performed, but the language is supported by a graphical interface that guides users through functions and options. We first show crossword’s utility in QTL-seq design, where its output accurately reflects empirical data. By introducing the concept of levels to reflect family relatedness, crossword is suitable to a broad range of breeding programs and crops. Using levels, we further illustrate crossword’s capabilities by examining the effect of family size and number of selfing generations on phenotyping accuracy and genomic selection. Additionally, we explore the ramifications of effect polarity among parents in a mapping cross, a scenario that is common in crop genetics but often difficult to simulate. Given the ease of use and apparent realism, we anticipate crossword will quickly become a “bicycle for the [geneticist’s] mind”.

On the Application of the Bay Model for Vortex Generator Flows

2018 ◽  
Author(s):  
Marinos Manolesos ◽  
Giorgos Papadakis ◽  
Spyros G. Voutsinas
Keyword(s):  
Wind Turbine ◽  
Model Simulation ◽  
Vortex Generator ◽  
Ease Of Use ◽  
Navier Stokes ◽  
Blade Design ◽  
Model Simulations ◽  
User Input ◽  
Wind Turbine Airfoil ◽  
Turbine Blade Design

Today, Vortex Generators (VGs) are becoming an integral part of a Wind Turbine blade design. However, the challenges that are involved in the computation of the flow around VGs are yet to be dealt with in a satisfactory manner. A large number of VG models for flow solvers have been proposed and among them, the BAY model is one of the most popular for its ease of use and relatively low requirements for user input. In the present paper, a thorough investigation on the performance and application of the BAY model for aerodynamic Vortex Generator flows is presented. A Fully Resolved Reynolds Averaged Navier Stokes simulation is validated against experiments and then used as the benchmark for the BAY model simulations. The Benchmark case is the flow past a wind turbine airfoil at Reynolds number 0.87e6. When the grid related errors are excluded, it is found that in the model simulations, the generated vortices are weaker than in the fully resolved computation. The latter finding is linked to an inherent deficiency of the model, which is explained in detail. As the vortex generation mechanism is different between the fully resolved and the BAY model simulation, so is the vortex evolution and interaction, even on the same numerical mesh. With regards to grid dependence, the integral BAY force depends on both grid density and grid architecture.

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