Annotation of multiple regions of interest across the whole mouse brain is an indispensable process for quantitative evaluation of a multitude of study endpoints in neuroscience digital pathology. Prior experience and domain expert knowledge are the key aspects for image annotation quality and consistency. At present, image annotation is often achieved manually by certified pathologists or trained technicians, limiting the total throughput of studies performed at neuroscience digital pathology labs. It may also mean that simpler and quicker methods of examining tissue samples are used by non-pathologists, especially in the early stages of research and preclinical studies. To address these limitations and to meet the growing demand for image analysis in a pharmaceutical setting, we developed AnNoBrainer, an open-source software tool that leverages deep learning, image registration, and standard cortical brain templates to automatically annotate individual brain regions on 2D pathology slides. Application of AnNoBrainer to a published set of pathology slides from transgenic mice models of synucleinopathy revealed comparable accuracy, increased reproducibility, and a significant reduction (~ 50%) in time spent on brain annotation, quality control and labelling compared to trained scientists in pathology. Taken together, AnNoBrainer offers a rapid, accurate, and reproducible automated annotation of mouse brain images that largely meets the experts' histopathological assessment standards (> 85% of cases) and enables high-throughput image analysis workflows in digital pathology labs.
Intravascular optical coherence tomography (IVOCT) is used to assess stent tissue coverage and malapposition in stent evaluation trials. We developed the OCT Image Visualization and Analysis Toolkit for Stent (OCTivat-Stent), for highly automated analysis of IVOCT pullbacks. Algorithms automatically detected the guidewire, lumen boundary, and stent struts; determined the presence of tissue coverage for each strut; and estimated the stent contour for comparison of stent and lumen area. Strut-level tissue thickness, tissue coverage area, and malapposition area were automatically quantified. The software was used to analyze 292 stent pullbacks. The concordance-correlation-coefficients of automatically measured stent and lumen areas and independent manual measurements were 0.97 and 0.99, respectively. Eleven percent of struts were missed by the software and some artifacts were miscalled as struts giving 1% false-positive strut detection. Eighty-two percent of uncovered struts and 99% of covered struts were labeled correctly, as compared to manual analysis. Using the highly automated software, analysis was harmonized, leading to a reduction of inter-observer variability by 30%. With software assistance, analysis time for a full stent analysis was reduced to less than 30 minutes. Application of this software to stent evaluation trials should enable faster, more reliable analysis with improved statistical power for comparing designs.
- MeSH
- endovaskulární výkony přístrojové vybavení metody MeSH
- lidé MeSH
- optická koherentní tomografie přístrojové vybavení metody MeSH
- senzitivita a specificita MeSH
- software normy MeSH
- stenty škodlivé účinky normy MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- hodnotící studie MeSH
- Research Support, N.I.H., Extramural MeSH
BACKGROUND: Simulators used in teaching are interactive applications comprising a mathematical model of the system under study and a graphical user interface (GUI) that allows the user to control the model inputs and visualize the model results in an intuitive and educational way. Well-designed simulators promote active learning, enhance problem-solving skills, and encourage collaboration and small group discussion. However, creating simulators for teaching purposes is a challenging process that requires many contributors including educators, modelers, graphic designers, and programmers. The availability of a toolchain of user-friendly software tools for building simulators can facilitate this complex task. OBJECTIVE: This paper aimed to describe an open-source software toolchain termed Bodylight.js that facilitates the creation of browser-based client-side simulators for teaching purposes, which are platform independent, do not require any installation, and can work offline. The toolchain interconnects state-of-the-art modeling tools with current Web technologies and is designed to be resilient to future changes in the software ecosystem. METHODS: We used several open-source Web technologies, namely, WebAssembly and JavaScript, combined with the power of the Modelica modeling language and deployed them on the internet with interactive animations built using Adobe Animate. RESULTS: Models are implemented in the Modelica language using either OpenModelica or Dassault Systèmes Dymola and exported to a standardized Functional Mock-up Unit (FMU) to ensure future compatibility. The C code from the FMU is further compiled to WebAssembly using Emscripten. Industry-standard Adobe Animate is used to create interactive animations. A new tool called Bodylight.js Composer was developed for the toolchain that enables one to create the final simulator by composing the GUI using animations, plots, and control elements in a drag-and-drop style and binding them to the model variables. The resulting simulators are stand-alone HyperText Markup Language files including JavaScript and WebAssembly. Several simulators for physiology education were created using the Bodylight.js toolchain and have been received with general acclaim by teachers and students alike, thus validating our approach. The Nephron, Circulation, and Pressure-Volume Loop simulators are presented in this paper. Bodylight.js is licensed under General Public License 3.0 and is free for anyone to use. CONCLUSIONS: Bodylight.js enables us to effectively develop teaching simulators. Armed with this technology, we intend to focus on the development of new simulators and interactive textbooks for medical education. Bodylight.js usage is not limited to developing simulators for medical education and can facilitate the development of simulators for teaching complex topics in a variety of different fields.
- MeSH
- internet MeSH
- lidé MeSH
- software normy MeSH
- studium lékařství metody MeSH
- uživatelské rozhraní počítače * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
We present the ROCA (ROad Curvature Analyst) software, in the form of an ESRI ArcGIS Toolbox, intended for vector line data processing. The software segments road network data into tangents and horizontal curves. Horizontal curve radii and azimuth of tangents are then automatically computed. Simultaneously, additional frequently used road section characteristics are calculated, such as the sinuosity of a road section (detour ratio), the number of turns along an individual road section and the average cumulative angle for a road section. The identification of curves is based on the naïve Bayes classifier and users are allowed to prepare their own training data files. We applied ROCA software to secondary roads within the Czech road network (9,980 km). The data processing took less than ten minutes. Approximately 43% of the road network in question consists of 42,752 horizontal curves. The ROCA software outperforms other existing automatic methods by 26% with respect to the percentage of correctly identified curves. The segmented secondary roads within the Czech road network can be viewed on the roca.cdvgis.cz/czechia web-map application. We combined data on road geometry with road crashes database to develop the crash modification factors for horizontal curves with various radii. We determined that horizontal curves with radii of 50 m are approximately 3.7 times more hazardous than horizontal curves with radii accounting for 1000 m. ROCA software can be freely downloaded for noncommercial use from https://roca.cdvinfo.cz/ website.
- MeSH
- automobily normy MeSH
- bezpečnost MeSH
- dopravní nehody prevence a kontrola MeSH
- geografické informační systémy MeSH
- lidé MeSH
- pomůcky pro sebeobsluhu * MeSH
- řízení motorových vozidel * normy MeSH
- rotace * MeSH
- rozpoznávání automatizované metody MeSH
- software * normy MeSH
- životní prostředí - projekt MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Motivation: The many thousands of high-quality genomes available now-a-days imply a shift from single genome to pan-genomic analyses. A basic algorithmic building brick for such a scenario is online search over a collection of similar texts, a problem with surprisingly few solutions presented so far. Results: We present SOPanG, a simple tool for exact pattern matching over an elastic-degenerate string, a recently proposed simplified model for the pan-genome. Thanks to bit-parallelism, it achieves pattern matching speeds above 400 MB/s, more than an order of magnitude higher than of other software. Availability and implementation: SOPanG is available for free from: https://github.com/MrAlexSee/sopang. Supplementary information: Supplementary data are available at Bioinformatics online.
- MeSH
- diabetes mellitus * farmakoterapie prevence a kontrola MeSH
- diabetická retinopatie farmakoterapie prevence a kontrola MeSH
- dlouhodobě působící inzulin farmakokinetika farmakologie terapeutické užití MeSH
- fixní kombinace léků * MeSH
- glukagonu podobný peptid 1 farmakokinetika farmakologie terapeutické užití MeSH
- inzulin aspart farmakokinetika farmakologie terapeutické užití MeSH
- inzuliny * klasifikace normy terapeutické užití MeSH
- klinické zkoušky, fáze III jako téma MeSH
- kongresy jako téma MeSH
- lidé MeSH
- liraglutid farmakokinetika farmakologie terapeutické užití MeSH
- metformin farmakokinetika farmakologie terapeutické užití MeSH
- software normy trendy zákonodárství a právo MeSH
- Check Tag
- lidé MeSH
In 2018 Polish health IT community faces critical challenges related to the national eHealth agenda. The mission of HL7 Poland is to establish a community around interoperability standards and integration profiles with health IT vendors, medical providers and public authorities. One of the activities that would support this goal is providing tooling for specification publication and implementation validation. HL7 Poland has started a project to create a central hub for specifications and tools. The Tukan is an online platform dedicated to Polish healthcare IT community, where national specifications for interoperability are published together with a set of testing tools supporting their implementation. The platform is based on software components originating from various sources: open source release of IHE Gazelle components, development tooling of Polish National Implementation Guide of HL7 CDA, ART-DECOR platform software components, HAPI FHIR reference implementation for FHIR STU3 standard and Central Authentication Server (CAS) software components. Tukan platform is ready to be used as an environment supporting peer-to-peer testing in connectathon-like events. The pilot phase of Tukan platform has shown that there is a significant interest in testing services, especially when there are official specifications of interoperability standards published. In 2018 the first Polish connectathon will be held by HL7 Poland on Tukan platform in cooperation with national and regional projects.
Electroencephalography (EEG)-the direct recording of the electrical activity of populations of neurons-is a tremendously important tool for diagnosing, treating, and researching epilepsy. Although standard procedures for recording and analyzing human EEG exist and are broadly accepted, there are no such standards for research in animal models of seizures and epilepsy-recording montages, acquisition systems, and processing algorithms may differ substantially among investigators and laboratories. The lack of standard procedures for acquiring and analyzing EEG from animal models of epilepsy hinders the interpretation of experimental results and reduces the ability of the scientific community to efficiently translate new experimental findings into clinical practice. Accordingly, the intention of this report is twofold: (1) to review current techniques for the collection and software-based analysis of neural field recordings in animal models of epilepsy, and (2) to offer pertinent standards and reporting guidelines for this research. Specifically, we review current techniques for signal acquisition, signal conditioning, signal processing, data storage, and data sharing, and include applicable recommendations to standardize collection and reporting. We close with a discussion of challenges and future opportunities, and include a supplemental report of currently available acquisition systems and analysis tools. This work represents a collaboration on behalf of the American Epilepsy Society/International League Against Epilepsy (AES/ILAE) Translational Task Force (TASK1-Workgroup 5), and is part of a larger effort to harmonize video-EEG interpretation and analysis methods across studies using in vivo and in vitro seizure and epilepsy models.
- MeSH
- elektroencefalografie * přístrojové vybavení metody normy MeSH
- epilepsie patofyziologie MeSH
- modely nemocí na zvířatech MeSH
- mozek patofyziologie MeSH
- poradní výbory * MeSH
- software * normy MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
- Research Support, N.I.H., Extramural MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
Background: Developed countries are planning the creation of national EHR (Electronic Health Record) systems to modernize the healthcare field and improve its quality, security and efficiency. Objectives: To support clinical data sharing, it is important that an EHR is designed to be integrated within an appropriate architectural context aimed to satisfy the needs of all actors involved in this information management by adding and integrating new functionalities to existing solutions. Methods: SOA (Service Oriented Architecture) provides a good approach to promote the easy integration and alignment of a new and existing solution into a cohesive architecture. The HSSP (Healthcare Service Specification Program) was formed to adopt the SOA approach to guarantee interoperability between applications and distributed and heterogeneous devices, by providing a set of standards to design and develop specific services. Results: The authors present a landscape architecture to support the collaboration between actors involved in the treatment of chronic diseases. The core of this architecture consists of services compliant to HSSP standards. Among these, the authors developed: Health Record Management Services, Health Terminology Services and Health Identity Services. The proposed architecture and these services have already been adopted in different systems: a telemonitoring system to support the continuity of care of CHF (Congestive Heart Failure) patients, two systems to share clinical data to manage clinical trials in both infectivology and ophthalmology. Conclusions: The main advantage of the proposed architecture is its flexibility that allows it to be adapted over time and to be adopted in all health care scenarios.
