open source software
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For decades, biologists have relied on software to visualize and interpret imaging data. As techniques for acquiring images increase in complexity, resulting in larger multidimensional datasets, imaging software must adapt. ImageJ is an open-source image analysis software platform that has aided researchers with a variety of image analysis applications, driven mainly by engaged and collaborative user and developer communities. The close collaboration between programmers and users has resulted in adaptations to accommodate new challenges in image analysis that address the needs of ImageJ's diverse user base. ImageJ consists of many components, some relevant primarily for developers and a vast collection of user-centric plugins. It is available in many forms, including the widely used Fiji distribution. We refer to this entire ImageJ codebase and community as the ImageJ ecosystem. Here we review the core features of this ecosystem and highlight how ImageJ has responded to imaging technology advancements with new plugins and tools in recent years. These plugins and tools have been developed to address user needs in several areas such as visualization, segmentation, and tracking of biological entities in large, complex datasets. Moreover, new capabilities for deep learning are being added to ImageJ, reflecting a shift in the bioimage analysis community towards exploiting artificial intelligence. These new tools have been facilitated by profound architectural changes to the ImageJ core brought about by the ImageJ2 project. Therefore, we also discuss the contributions of ImageJ2 to enhancing multidimensional image processing and interoperability in the ImageJ ecosystem.
- Klíčová slova
- Fiji, ImageJ, image analysis, imaging, microscopy, open source software,
- MeSH
- počítačové zpracování obrazu * MeSH
- software * MeSH
- umělá inteligence * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
Open source paradigm is becoming widely accepted in scientific communities and open source hardware is finding its steady place in chemistry research. In this review article, we provide the reader with the most up-to-date information on open source hardware and software resources enabling the construction and utilization of an "open source capillary electrophoresis instrument". While CE is still underused as a separation technique, it offers unique flexibility, low-cost, and high efficiency and is particularly suitable for open source instrumental development. We overview the major parts of CE instruments, such as high voltage power supplies, detectors, data acquisition systems, and CE software resources with emphasis on availability of the open source information on the web and in the scientific literature. This review is the first of its kind, revealing accessible blueprints of most parts from which a fully functional open source CE system can be built. By collecting the extensive information on open source capillary electrophoresis in this review article, the authors aim at facilitating the dissemination of knowledge on CE within and outside the scientific community, fosters innovation and inspire other researchers to improve the shared CE blueprints.
- Klíčová slova
- Capillary electrophoresis, Open source hardware, Open source software, Review,
- MeSH
- design vybavení MeSH
- elektroforéza kapilární přístrojové vybavení MeSH
- elektronika přístrojové vybavení MeSH
- software MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
Benchmarking and monitoring of urban design and transport features is crucial to achieving local and international health and sustainability goals. However, most urban indicator frameworks use coarse spatial scales that either only allow between-city comparisons, or require expensive, technical, local spatial analyses for within-city comparisons. This study developed a reusable, open-source urban indicator computational framework using open data to enable consistent local and global comparative analyses. We show this framework by calculating spatial indicators-for 25 diverse cities in 19 countries-of urban design and transport features that support health and sustainability. We link these indicators to cities' policy contexts, and identify populations living above and below critical thresholds for physical activity through walking. Efforts to broaden participation in crowdsourcing data and to calculate globally consistent indicators are essential for planning evidence-informed urban interventions, monitoring policy effects, and learning lessons from peer cities to achieve health, equity, and sustainability goals.
- MeSH
- celosvětové zdraví * MeSH
- lidé MeSH
- prostorová analýza MeSH
- software MeSH
- velkoměsta MeSH
- zdravotní stav * MeSH
- Check Tag
- lidé 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, P.H.S. MeSH
- Geografické názvy
- velkoměsta MeSH
In this short report we introduce DigitalVHI, a free open-source software application for obtaining Voice Handicap Index (VHI) and other questionnaire data, which can be put on a computer in clinics and used in clinical practice. The software can simplify performing clinical studies since it makes the VHI scores directly available for analysis in a digital form. It can be downloaded from http://www.christian-herbst.org/DigitalVHI/.
- Klíčová slova
- Voice Handicap Index, digital, questionnaire, software application,
- MeSH
- akustika * MeSH
- jazyk (prostředek komunikace) * MeSH
- kvalita hlasu * MeSH
- lidé MeSH
- měření tvorby řeči metody MeSH
- počítačová grafika MeSH
- počítačové zpracování signálu * MeSH
- poruchy hlasu diagnóza patofyziologie MeSH
- posuzování pracovní neschopnosti * MeSH
- prediktivní hodnota testů MeSH
- prognóza MeSH
- průzkumy a dotazníky MeSH
- software * MeSH
- stupeň závažnosti nemoci MeSH
- uživatelské rozhraní počítače MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The growing technical standard of acquisition systems allows the acquisition of large records, often reaching gigabytes or more in size as is the case with whole-day electroencephalograph (EEG) recordings, for example. Although current 64-bit software for signal processing is able to process (e.g. filter, analyze, etc) such data, visual inspection and labeling will probably suffer from rather long latency during the rendering of large portions of recorded signals. For this reason, we have developed SignalPlant-a stand-alone application for signal inspection, labeling and processing. The main motivation was to supply investigators with a tool allowing fast and interactive work with large multichannel records produced by EEG, electrocardiograph and similar devices. The rendering latency was compared with EEGLAB and proves significantly faster when displaying an image from a large number of samples (e.g. 163-times faster for 75 × 10(6) samples). The presented SignalPlant software is available free and does not depend on any other computation software. Furthermore, it can be extended with plugins by third parties ensuring its adaptability to future research tasks and new data formats.
[Statistical software--review of current products]
The paper gives an objective sight on extent variety of submitted statistical packages. It's especially evaluated range and quality of statistical methods, user environment and graphical facility of software. The paper brings information which is dispersed in many sources and therefore is hardly accessible.
- MeSH
- software * MeSH
- statistika jako téma * MeSH
- Publikační typ
- anglický abstrakt MeSH
- časopisecké články MeSH
The authors give an account of different types of commercially supplied programmes which can be used also in the health services. They discuss the properties and types of different software - data base programmes, text processors, graphic and statistical programmes and finally so-called integrated software along with data on possible mutual combinations. At the same time also general conditions for the application of these programmes within the framework of clinical informations systems are discussed incl. their advantages and short-comings.
- MeSH
- lékařská informatika * MeSH
- software * MeSH
- Publikační typ
- anglický abstrakt MeSH
- časopisecké články MeSH
Scoring thermal tolerance traits live or with recorded video can be time consuming and susceptible to observer bias, and as with many physiological measurements, there can be trade-offs between accuracy and throughput. Recent studies show that automated particle tracking is a viable alternative to manually scoring videos, although some of the software options are proprietary and costly. In this study, we present a novel strategy for automated scoring of thermal tolerance videos by inferring motor activity with motion detection using an open-source Python command line application called DIME (detector of insect motion endpoint). We apply our strategy to both dynamic and static thermal tolerance assays, and our results indicate that DIME can accurately measure thermal acclimation responses, generally agrees with visual estimates of thermal limits, and can significantly increase throughput over manual methods.
- Klíčová slova
- Automated particle tracking, Automatic scoring, Bioassay, Motor performance, Thermal limits,
- MeSH
- aklimatizace * MeSH
- hmyz MeSH
- počítače MeSH
- pohyb těles MeSH
- software * MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
Light simulations hold great potential for advancing optical techniques in neuroscience. They facilitate the in-silico refinement of optical stimulator designs and enable simulations of optical recordings from computational brain models, aiding neuroscience in forming a mechanistic understanding of brain circuitry. However, many published light models are inaccessible due to unavailable source code and documentation or are impractical due to excessive computational demands. To address these challenges, we replicate and enhance the efficient and accurate light simulation model by Yona et al. [1], which was previously available only in compiled form accompanied by sparse documentation. In this work, we resolve ambiguities in the original model, correct errors that caused discrepancies between simulations and published results, improve computational efficiency by an order of magnitude, and open-source all the resulting code and detailed documentation. These enhancements enable simulations of cortical volumes exceeding [Formula: see text] to run in seconds on standard laptop hardware. Our model software provides an accessible, adaptable, and rapid light simulation tool, which adheres to FAIR principles to ensure future-proof and broad utility for the neuroscience community.
- MeSH
- lidé MeSH
- modely neurologické * MeSH
- mozek * fyziologie MeSH
- počítačová simulace MeSH
- software * MeSH
- světlo * MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
With ongoing global climate change and an increasingly urbanized population, the importance of city parks and other forms of urban vegetation increases. Trees in urban parks can play an important role in mitigating runoff and delivering other ecosystem services. Park managers, E-NGOs, citizen scientists and others are increasingly called upon to evaluate the possible consequences of changes in park management such as, e.g., tree removal. Here, we present an unorthodox approach to hydrological modelling and its potential use in local policy making regarding urban greenery. The approach consists of a minimalist field campaign to characterize vegetation and soil moisture status combined with a novel model calibration using freely available data and software. During modelling, we were able to obtain coefficients of determination (R2) of 0.66 and 0.73 for probe-measured and simulated soil moisture under tree stand and park lawn land covers respectively. The results demonstrated that tree cover had a significant positive effect on the hydrological regime of the locality through interception, transpiration and effects on soil moisture. Simulations suggested that tree cover was twice as effective at mitigating runoff than park lawn and almost seven times better than impervious surfaces. In the case of a potential replacement of tree vegetation in favour of park lawn or impervious surfaces an increase in runoff of 14% and 81% respectively could be expected. The main conclusion drawn from our study was that such an approach can be a very useful tool for supporting local decision-making processes as it offers a freely available, cheap and relatively easy-to-use way to describe the hydrological consequences of landcover change (e.g., tree removal) with sufficient accuracy.
- Klíčová slova
- Ecohydrological services, Green infrastructure, Open data, Open science, Runoff modelling, Urban greenery,
- MeSH
- ekosystém MeSH
- hydrologie MeSH
- software * MeSH
- stromy * MeSH
- velkoměsta MeSH
- veřejné parky * MeSH
- zachování přírodních zdrojů metody MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Česká republika MeSH
- velkoměsta MeSH
