Search results for "Workflow"
showing 10 items of 133 documents
Effects of DBS in parkinsonian patients depend on the structural integrity of frontal cortex
2017
AbstractWhile deep brain stimulation of the subthalamic nucleus (STN-DBS) has evolved to an evidence-based standard treatment for Parkinson’s disease (PD), the targeted cerebral networks are poorly described and no objective predictors for the postoperative clinical response exist. To elucidate the systemic mechanisms of DBS, we analysed cerebral grey matter properties using cortical thickness measurements and addressed the dependence of structural integrity on clinical outcome. Thirty one patients with idiopathic PD without dementia (23 males, age: 63.4 ± 9.3, Hoehn and Yahr: 3.5 ± 0.8) were selected for DBS treatment. The patients underwent whole-brain preoperative T1 MR-Imaging at 3 T. G…
Simple Muscle Architecture Analysis (SMA): An ImageJ macro tool to automate measurements in B-mode ultrasound scans
2020
In vivo measurements of muscle architecture (i.e. the spatial arrangement of muscle fascicles) are routinely included in research and clinical settings to monitor muscle structure, function and plasticity. However, in most cases such measurements are performed manually, and more reliable and time-efficient automated methods are either lacking completely, or are inaccessible to those without expertise in image analysis. In this work, we propose an ImageJ script to automate the entire analysis process of muscle architecture in ultrasound images: Simple Muscle Architecture Analysis (SMA). Images are filtered in the spatial and frequency domains with built-in commands and external plugins to hi…
Graphical Workflow System for Modification Calling by Machine Learning of Reverse Transcription Signatures
2019
Modification mapping from cDNA data has become a tremendously important approach in epitranscriptomics. So-called reverse transcription signatures in cDNA contain information on the position and nature of their causative RNA modifications. Data mining of, e.g. Illumina-based high-throughput sequencing data, is therefore fast growing in importance, and the field is still lacking effective tools. Here we present a versatile user-friendly graphical workflow system for modification calling based on machine learning. The workflow commences with a principal module for trimming, mapping, and postprocessing. The latter includes a quantification of mismatch and arrest rates with single-nucleotide re…
Application of a portable instrument for rapid and reliable detection of SARS-CoV-2 infection in any environment
2020
Abstract The ongoing outbreak of the novel coronavirus (SARS‐CoV‐2) infection is creating serious challenges for health laboratories that seek to identify viral infections as early as possible, optimally at the earliest appearance of symptom. Indeed, there is urgent need to develop and deploy robust diagnostic methodologies not only to use in health laboratory environments but also directly in places where humans circulate and spread the virus such as airports, trains, boats, and any public aggregation places. The success of a reliable and sensitive asymptomatic diagnosis relies on the identification and measurement of informative biomarkers from human host and virus in a rapid, sensitive, …
How to Write Ethical User Stories? : Impacts of the ECCOLA Method
2021
AbstractArtificial Intelligence (AI) systems are increasing in significance within software services. Unfortunately, these systems are not flawless. Their faults, failures and other systemic issues have emphasized the urgency for consideration of ethical standards and practices in AI engineering. Despite the growing number of studies in AI ethics, comparatively little attention has been placed on how ethical issues can be mitigated in software engineering (SE) practice. Currently understanding is lacking regarding the provision of useful tools that can help companies transform high-level ethical guidelines for AI ethics into the actual workflow of developers. In this paper, we explore the i…
Main Steps in Image Processing and Quantification: The Analysis Workflow
2019
In the last decades, the variety of programs, algorithms, and strategies that researchers have at their disposal to process and analyze image files has grown extensively. However, these are only pointless tools if not applied with the careful planning required to achieve a succesful image analysis. In order to do so, the analyst must establish a meaningful and effective sequence of orderly operations that is able to (1) overcome all the problems derived from the image manipulation and (2) successfully resolve the question that was originally posed. In this chapter, the authors suggest a set of strategies and present a reflection on the main milestones that compose the image processing workf…
Using UAV Based 3D Modelling to Provide Smart Monitoring of Road Pavement Conditions
2020
Road pavements need adequate maintenance to ensure that their conditions are kept in a good state throughout their lifespans. For this to be possible, authorities need efficient and effective databases in place, which have up to date and relevant road condition information. However, obtaining this information can be very difficult and costly and for smart city applications, it is vital. Currently, many authorities make maintenance decisions by assuming road conditions, which leads to poor maintenance plans and strategies. This study explores a pathway to obtain key information on a roadway utilizing drone imagery to replicate the roadway as a 3D model. The study validates this by using stru…
Towards Quantifying Non-Photosynthetic Vegetation for Agriculture Using Spaceborne Imaging Spectroscopy
2021
Non-photosynthetic vegetation (NPV) has been identified as priority variable in the context of new spaceborne imaging spectroscopy missions. In this study we provide a first attempt to quantify NPV biomass from these unprecedented data streams to be provided by multiple recently launched or planned instruments. A hybrid workflow is proposed including Gaussian process regression (GPR) trained over radiative transfer model (RTM) simulations and applying active learning strategies. A soybean field data set including two dates with NPV measurements on yellow and senescent (brown) plant organs was used for model validation, resulting in relative errors of 13.4%. This prototype retrieval model wa…
The European COVID-19 drugs calculation tool: an aid for the estimation of the drugs needed during the SARS-CoV 2 pandemic
2021
Objective To create an informatics supportive tool, which can assist healthcare professionals in estimating potential requirements for essential drug supplies to respond to the current SARS-CoV-2 pandemic based on epidemiological forecasting. Methods The tool was based on a Susceptible-Infected-Removed (SIR) epidemiological model in which the population is divided into three compartments and transmission parameters are specified to define the rate at which people move between stages. Appropriate data entry was guaranteed by the creation of structured guided paths. The drugs needed for the forecasted patients were estimated according to a list of critical care drugs compiled by consulting pr…
Vision metrology and Structure from Motion for archaeological heritage 3D reconstruction: A Case Study of various Roman mosaics
2017
<p class="Abstract">Vision metrology and computer vision can be successfully used for archaeological heritage 3D reconstruction in very high precision 3D measurement projects. Of those archaeological objects requiring very accurate measurements (&lt;1 mm), ancient mosaics comprise some of the most important. The aim of this paper is to assess the photogrammetric/computer vision approach in a vision metrology context as part of a 3D mosaics survey. In order to evaluate the optimal photogrammetric/computer vision workflow in this work, three different surveys were performed on three mosaics of different sizes and locations. Two of these are stored at the <em>Antonino Salinas&l…