A High-Resolution LED Stimulator for Steady-State Visual Stimulation: Customizable, Affordable, and Open Source.

Visually evoked steady-state potentials (SSVEPs) are neural responses elicited by visual stimuli oscillating at specific frequencies. In this study, we introduce a novel LED stimulator system explicitly designed for steady-state visual stimulation, offering precise control over visual stimulus parameters, including frequency resolution, luminance, and the ability to control the phase at the end of the stimulation. The LED stimulator provides a personalized, modular, and affordable option for experimental setups. Based on the Teensy 3.2 board, the stimulator utilizes direct digital synthesis and pulse width modulation techniques to control the LEDs. We validated its performance through four experiments: the first two measured LED light intensities directly, while the last two assessed the stimulator's impact on EEG recordings. The results demonstrate that the stimulator can deliver a stimulus suitable for generating SSVEPs with the desired frequency and phase resolution. As an open source resource, we provide comprehensive documentation, including all necessary codes and electrical diagrams, which facilitates the system's replication and adaptation for specific experimental requirements, enhancing its potential for widespread use in the field of neuroscience setups.

Combining methods to conduct a systematic review and propose a conceptual and theoretical framework in socio-environmental research.

This study aims to present a combination of methods and propose robust theoretical and conceptual frameworks for solving socio-environmental issues. This proposal included the Problem, Intervention, Context, and Outcome (PICO) framework and Protocol and Reporting result with Search, Appraisal, Synthesis, and Analysis framework, and develop (PSALSAR) method through SODIP steps: (i) Systematic review and meta-analysis defining the study from guiding questions; (ii) Open-source related to software and data; (iii) Data visualization and design information; (iv) Identification of gaps, challenges and trends through automation and lexicometric analysis; and (v) Proposal of theoretical and conceptual frameworks. This proposal defines the steps as support to combine and systematize information necessary to facilitate the production of this type of document using open-access software in the visualization and design of information. All these steps are replicable and essential to propose a conceptual and theoretical framework to contribute to the construction of knowledge in socio-environmental research and to propose solutions by filling in the gaps. In summary, this combination of methods shows:•The use of SODIP steps provides robustness and efficiency in carrying out review studies, facilitating the way to propose theoretical or conceptual frameworks.•Choosing to use open-source tools is essential for better evaluation and visualization of qualitative and quantitative data in review studies.•The combination of methods and data in the systematic review (scientific, political documents. and databases) supports the proposal of robust theoretical and conceptual frameworks.

Development and construction of an open-platform, open-source low-cost portable uroflowmeter: The OpenFlow device.

BACKGROUND: Uroflowmetry is useful to screen for and manage many voiding disorders. Home-based uroflowmetry might better represent the patient's true voiding pattern and be more widely adopted if an accurate low-cost portable device was available. OBJECTIVE: Development and initial evaluation of an open-platform, open-source low-cost portable uroflowmeter. MATERIALS AND METHODS: We designed and built an uroflowmeter comprising of a load cell and digital memory card unit connected to a programmable microcontroller board mounted upon a 3D printed frame. It generated date-stamped tables which were processed and plotted. Twenty urologists were recruited to assess the device. Each participant received the equipment that was returned, along with a bladder diary, after at least 24 consecutive hours of homemade uroflowmetry recording. Additionally, were assessed with the International Prostatic Symptom Score (I-PSS) and Peeling diagram, whereas the device's ease of use, robustness, and portability were evaluated with a Likert-type questionnaire. Two experienced urodynamicists independently evaluated the tracings' quality rated with a 3° ordinal scale: (1) Interpretable without artifacts; (2) Interpretable with artifacts; (3) Uninterpretable. RESULTS: Participants' median age was 36.6 years old, none having an I-PSS > 5 or Peeling > 2. Overall 138 voidings were recorded (77 daytime, 61 nightly episodes). The device's ease of use, robustness, and portability obtained maximum score in 80% of evaluations. Most (98%) of the tracings were considered interpretable. Limitations included its small study population and short monitoring times. CONCLUSION: The construction of a cheap (<50 USD), accurate user-friendly portable uroflowmeter proved feasible, which could facilitate access to portable uroflowmetry.

Particle Tracking and Micromixing Performance Characterization with a Mobile Device.

Strategies to stir and mix reagents in microfluid devices have evolved concomitantly with advancements in manufacturing techniques and sensing. While there is a large array of reported designs to combine and homogenize liquids, most of the characterization has been focused on setups with two inlets and one outlet. While this configuration is helpful to directly evaluate the effects of features and parameters on the mixing degree, it does not portray the conditions for experiments that involve more than two substances required to be subsequently combined. In this work, we present a mixing characterization methodology based on particle tracking as an alternative to the most common approach to measure homogeneity using the standard deviation of pixel intensities from a grayscale image. The proposed algorithm is implemented on a free and open-source mobile application (MIQUOD) for Android devices, numerically tested on COMSOL Multiphysics, and experimentally tested on a bidimensional split and recombine micromixer and a three-dimensional micromixer with sinusoidal grooves for different Reynolds numbers and geometrical features for samples with fluids seeded with red, blue, and green microparticles. The application uses concentration field data and particle track data to evaluate up to eleven performance metrics. Furthermore, with the insights from the experimental and numerical data, a mixing index for particles (mp) is proposed to characterize mixing performance for scenarios with multiple input reagents.

Monitoring multiple parameters in complex water scenarios using a low-cost open-source data acquisition platform.

Water monitoring faces challenges that are driven by the infrastructure, protection, financial resources, science and innovation policies, among others. A modular, low-cost, fully open-source and small-sized Unmanned Surface Vessel (USV) called EMAC-USV (EMAC: Estación de Monitoreo Ambiental Costero), is proposed for monitoring bathymetry and water quality parameters (i.e. temperature, suspended solids concentration and hydrocarbon concentration) in complex water scenarios. A detailed description of each part of the platform as well as all electronic connections and functioning is presented.The field works were carried out in two small waste stabilization ponds and in a portion of the main tidal channel of the Bahía Blanca port. The EMAC-USV is the result of a cautious design, regarding the balancing performance, communications, payload capacity, among others.

El renacimiento tecnológico de la Radiología: la revolución open source y la inteligencia artificial

El campo de la radiología ha experimentado avances notables en las últimas décadas, con desarrollos que van desde la mejora de la calidad y digitalización de las imágenes hasta la detección asistida por computadora. Particularmente, la aparición de técnicas de Inteligencia Artificial basadas en Deep Learning y Visión Computacional han promovido soluciones innovadoras en el diagnóstico y el análisis radiológico. Se explora la relevancia de los desarrollos y modelos open source en el progreso de estas técnicas, resaltando el impacto que la colaboración y el acceso abierto han tenido en el avance científico del campo. La investigación tiene un enfoque cualitativo, con alcance descriptivo y retrospectivo, de corte longitudinal. Se realizó un análisis documental de la evolución y el impacto del open source en la Radiología, poniendo de relieve la colaboración multidisciplinar. Se examinaron casos de uso, ventajas, desafíos y consideraciones éticas en relación con la implementación de soluciones basadas en Inteligencia Artificial en Radiología. El enfoque open source ha mostrado ser una influencia positiva en la Radiología, con potencial para influir en la atención médica, ofreciendo soluciones más precisas y accesibles. No obstante, se presentan desafíos éticos y técnicos que requieren atención.

The field of radiology has seen notable advances in recent decades, with developments ranging from image quality improvement and digitization to computer-aided detection. Particularly, the emergence of Artificial Intelligence techniques based on Deep Learning and Computer Vision have promoted innovative solutions in diagnosis and radiological analysis. This article explores the relevance of open source developments and models in the progress of these techniques, highlighting the impact that collaboration and open access have had on the scientific advancement in this field. This research has a qualitative approach, with a descriptive, retrospective, longitudinal scope. A documentary analysis of the evolution and impact of open source in Radiology was carried out, highlighting multidisciplinary collaboration. Use cases, advantages, challenges and ethical considerations were also examined in relation to the implementation of AI-based solutions in Radiology. The Open Source approach has been shown to be a positive influence in Radiology, with the potential to influence medical care, offering more precise and accessible solutions. However, there are ethical and technical challenges that require attention.

Environmental scanning of cocaine trafficking in Brazil: Evidence from geospatial intelligence and natural language processing methods.

Cocaine trafficking threatens countries' national security and is a major public health challenge. Cocaine is transported from producer countries to consumer markets using various routes, methods, and transportation means. These routes develop in the geographical environment, are carefully planned and are geo-strategic objects that respond to the opportunities that drug trafficking organisations (DTOs) find to reduce the risks of interdiction. In this sense, individual drug seizure data (IDS) become essential indicators for identifying trends and understanding trafficking flows associated with drug trafficking routes. However, due to the illicit nature of DTOs, the availability of these data is considerably limited, hindering the ability to analyse and identify trends. This study presents a methodology for collecting and processing data from open-source information reported by Brazil's federal government news website. Using geospatial intelligence and natural language processing methods, we created a dataset with 939 records and 44 variables related to cocaine seizures in Brazil in 2022. We applied geospatial analysis techniques from this dataset to identify trends and potential cocaine trafficking flows. The results were broadly consistent with existing literature on drug trafficking. They demonstrated the potential of open-source information for environmental scanning and knowledge generation through geographic information science. The approach proposed in our research provides tools that can be used to complement drug trafficking monitoring and formulate public policies to strengthen prevention and enforcement strategies.

A web-based software for group decision with analytic hierarchy process.

The Analytic Hierarchy Process (AHP) is a multi-criteria decision support method and is widely applied in many areas. The original AHP method proposed by Thomas L. Saaty in the 1970s requires (n²-n)/2 comparisons. The number of required comparisons can make using this method challenging for maintaining consistent judgments in problems involving many criteria and/or alternatives. Furthermore, the available software is platform-dependent and generally does not support group decision-making. In this paper, we present software for AHP that demands n-1 comparisons. Additionally, the software supports group decision-making using individual aggregation of priorities with arithmetic and geometric means. The system is available at http://ahpweb.net/ and is accessible from any internet-connected device. It currently has more than 100 users and dozens of decision problems in various areas.•The original AHP formulation requires (n²-n)/2 comparisons per cluster which makes it difficult to make consistent judgments.•AHP avaliable software does not enable group decision making.•The proposed system AHP-WEB fills these gaps. The method demands n-1 comparisons per cluster without any inconsistency and allows group decision making on a web system.

RaspyControl Lab: A fully open-source and real-time remote laboratory for education in automatic control systems using Raspberry Pi and Python.

Currently, remote laboratories have gained relevance in engineering education as tools to support active learning, experimentation, and motivation of students. Nonetheless, the costs and issues regarding their implementation and deployment limit the access of the students and educators to their advantages and features such as technical and educational. In this line, this study describes a fully open-source remote laboratory in hardware and software for education in automatic control systems employing Raspberry Pi and Python language with an approximate cost of USD 461. Even, by changing some components, the cost can be reduced to USD 420 or less. To illustrate the functionalities of the laboratory, we proposed a low-cost tank control system with its respective instrumentation, signal conditioning, identification, and control, which are exposed in this document. However, other experiments can be easily scalable and adaptable to the remote laboratory. Concerning the interface of the laboratory, we designed a complete user-friendly web interface with real-time video for the users to perform the different activities in automatic control such as identification or controller implementation through the programming language Python. The instructions to build and replicate the hardware and software are indicated in the open repositories provided for the project as well as in this paper. Our intention with this project is to offer a complete low-cost and open-source remote laboratory that can be adapted and used for the students, educators, and stakeholders to learn, experiment, and teach in the field of automatic control systems.

Strategies to obtain a better quality of environmental data gathered by low cost systems.

Monitoring systems are ubiquitous in many environmental science fields due to the technological advances in the last decades, which contributed to the migration from conventional to automated observing networks. However, the cost of acquisition and operation of sensor networks is still a limiting factor for their wide use. Under this scenario, low-cost and affordable open-source sensors and systems emerge as an alternative to research-grade instruments. To fulfill the quality requirements defined by international organizations, sensor calibration has to be performed and shall be considered as a basic requirement. Best monitoring practices including established quality control procedures should be implemented for gathering environmental data. With a focus on data gathering, this paper reviews basic concepts on open source technologies, calibration methods, quality control procedures, applications and trends, and possibilities for improving the hardware of low-cost and affordable systems.

Human cortical amygdala dendrites and spines morphology under open-source three-dimensional reconstruction procedures.

Visualizing nerve cells has been fundamental for the systematic description of brain structure and function in humans and other species. Different approaches aimed to unravel the morphological features of neuron types and diversity. The inherent complexity of the human nervous tissue and the need for proper histological processing have made studying human dendrites and spines challenging in postmortem samples. In this study, we used Golgi data and open-source software for 3D image reconstruction of human neurons from the cortical amygdaloid nucleus to show different dendrites and pleomorphic spines at different angles. Procedures required minimal equipment and generated high-quality images for differently shaped cells. We used the "single-section" Golgi method adapted for the human brain to engender 3D reconstructed images of the neuronal cell body and the dendritic ramification by adopting a neuronal tracing procedure. In addition, we elaborated 3D reconstructions to visualize heterogeneous dendritic spines using a supervised machine learning-based algorithm for image segmentation. These tools provided an additional upgrade and enhanced visual display of information related to the spatial orientation of dendritic branches and for dendritic spines of varied sizes and shapes in these human subcortical neurons. This same approach can be adapted for other techniques, areas of the central or peripheral nervous system, and comparative analysis between species.

Stmol: A component for building interactive molecular visualizations within streamlit web-applications.

Streamlit is an open-source Python coding framework for building web-applications or "web-apps" and is now being used by researchers to share large data sets from published studies and other resources. Here we present Stmol, an easy-to-use component for rendering interactive 3D molecular visualizations of protein and ligand structures within Streamlit web-apps. Stmol can render protein and ligand structures with just a few lines of Python code by utilizing popular visualization libraries, currently Py3DMol and Speck. On the user-end, Stmol does not require expertise to interactively navigate. On the developer-end, Stmol can be easily integrated within structural bioinformatic and cheminformatic pipelines to provide a simple means for user-end researchers to advance biological studies and drug discovery efforts. In this paper, we highlight a few examples of how Stmol has already been utilized by scientific communities to share interactive molecular visualizations of protein and ligand structures from known open databases. We hope Stmol will be used by researchers to build additional open-sourced web-apps to benefit current and future generations of scientists.

A Low-Power IoT Device for Measuring Water Table Levels and Soil Moisture to Ease Increased Crop Yields.

The simultaneous measurement of soil water content and water table levels is of great agronomic and hydrological interest. Not only does soil moisture represent the water available for plant growth but also water table levels can affect crop productivity. Furthermore, monitoring soil saturation and water table levels is essential for an early warning of extreme rainfall situations. However, the measurement of these parameters employing commercial instruments has certain disadvantages, with a high cost of purchase and maintenance. In addition, the handling of commercial devices makes it difficult to adapt them to the specific requirements of farmers or decision-makers. Open-source IoT hardware platforms are emerging as an attractive alternative to developing flexible and low-cost devices. This paper describes the design of a datalogger device based on open-source hardware platforms to register water table levels and soil moisture data for agronomic applications. The paper begins by describing energy-saving and wireless transmission techniques. Then, it summarizes the linear calibration of the phreatimeter sensor obtained with laboratory and field data. Finally, it shows how non-linear machine-learning techniques improve predictions over classical tools for the moisture sensor (SKU: SEN0193).

PytuTester: RaspberryPi open-source ventilator tester.

PytuTester is an open-source ventilator tester developed to help bio-engineers in the design and verification of new ventilator prototypes. A ventilator tester allows measuring the flow, pressure, volume, and oxygen concentration provided to the patient. During the global pandemic COVID-19, several open-source ventilators prototypes were developed; however, due to high cost and demand testers, they were not available. In this context, a low-cost tester was developed using a Raspberry Pi and medical-grade sensors for the test ventilators prototypes. This paper presents the design files, software interface, and validations tests. Our results indicate that the tester has good accuracy to evaluate the efficacy and performance of new prototypes. When tested on two ventilator designs developed in Paraguay, PytuTester reported flow profiles that were concordant with the industry-standard VT650 Gas Flow Analyzer. PytuTester was then field deployed to test several DIY ventilator designs in low-resource areas.

An open-source, ready-to-use and validated ripple detector plugin for the Open Ephys GUI.

Objective. Sharp wave-ripples (SWRs, 100-250 Hz) are oscillatory events extracellularly recorded in the CA1 subfield of the hippocampus during sleep and quiet wakefulness. Many studies employed closed-loop strategies to either detect and abolish SWRs within the hippocampus or manipulate other relevant areas upon ripple detection. However, the code and schematics necessary to replicate the detection system are not always available, which hinders the reproducibility of experiments among different research groups. Furthermore, information about performance is not usually reported. Here, we sought to provide an open-source, validated ripple detector for the scientific community.Approach. We developed and validated a ripple detection plugin integrated into the Open Ephys graphical user's interface. It contains a built-in movement detector based on accelerometer or electromyogram data that prevents false ripple events (due to chewing, grooming, or moving, for instance) from triggering the stimulation/manipulation device.Main results. To determine the accuracy of the detection algorithm, we first carried out simulations in MATLAB with real ripple recordings. Using a specific combination of detection parameters (amplitude threshold of 5 standard deviations above the mean, time threshold of 10 ms, and root mean square block size of 7 samples), we obtained a 97% true positive rate and 2.48 false positives per minute. Next, an Open Ephys plugin based on the same detection algorithm was developed, and a closed-loop system was set up to evaluate the round trip (ripple onset-to-stimulation) latency over synthetic data. The lowest latency obtained was 34.5 ± 0.5 ms. The embedded movement monitoring was effective in reducing false positives and the plugin's flexibility to detect pathological events was also verified.Significance. Besides contributing to increased reproducibility, we anticipate that the developed ripple detector plugin will be helpful for many closed-loop applications in the field of systems neuroscience.

RT Box card for studying the control communication impacts on microgrid performance and stability.

This work presents the design process of an RT Box interface for control systems in microgrid applications. The control card allows implementing different controls and communication systems for microgrids in a physical environment, facilitating the development of robust control systems facing inherent adverse scenarios such as delays, loss of information packets, failures of partial or permanent communication and noise in signal overflows, among others. In addition, it permits the generation of programming resources and behavioral antecedents, helpful information for future users of the control card interface. The Plecs RT Box is a device that will enable a real-time simulation of different power electronics applications as can be a microgrid system. The built-in control card in this project is suitable as a complementary element of the RT Box, extending the capacity of this device to emulate a microgrid but testing real communication protocol between the microcontrollers that compose each of the distributed generation units (DGU). Tests were conducted to probe the communication protocols working correctly in a microgrid context, recreating real application scenarios.

IRimage: open source software for processing images from infrared thermal cameras.

IRimage aims at increasing throughput, accuracy and reproducibility of results obtained from thermal images, especially those produced with affordable, consumer-oriented cameras. IRimage processes thermal images, extracting raw data and calculating temperature values with an open and fully documented algorithm, making this data available for further processing using image analysis software. It also allows the making of reproducible measurements of the temperature of objects in a series of images, and produce visual outputs (images and videos) suitable for scientific reporting. IRimage is implemented in a scripting language of the scientific image analysis software ImageJ, allowing its use through a graphical user interface and also allowing for an easy modification or expansion of its functionality. IRimage's results were consistent with those of standard software for 15 camera models of the most widely used brand. An example use case is also presented, in which IRimage was used to efficiently process hundreds of thermal images to reveal subtle differences in the daily pattern of leaf temperature of plants subjected to different soil water contents. IRimage's functionalities make it better suited for research purposes than many currently available alternatives, and could contribute to making affordable consumer-grade thermal cameras useful for reproducible research.

Progress on open chemoinformatic tools for expanding and exploring the chemical space.

The concept of chemical space is a cornerstone in chemoinformatics, and it has broad conceptual and practical applicability in many areas of chemistry, including drug design and discovery. One of the most considerable impacts is in the study of structure-property relationships where the property can be a biological activity or any other characteristic of interest to a particular chemistry discipline. The chemical space is highly dependent on the molecular representation that is also a cornerstone concept in computational chemistry. Herein, we discuss the recent progress on chemoinformatic tools developed to expand and characterize the chemical space of compound data sets using different types of molecular representations, generate visual representations of such spaces, and explore structure-property relationships in the context of chemical spaces. We emphasize the development of methods and freely available tools focusing on drug discovery applications. We also comment on the general advantages and shortcomings of using freely available and easy-to-use tools and discuss the value of using such open resources for research, education, and scientific dissemination.

Mass grave localization prediction with geographical information systems in Guatemala and future impacts.

Conducting physical searches for mass grave locations based on anecdotal evidence is a time-consuming and resource-intensive endeavor in circumstances that often pose a threat to personal safety. The development of tools and procedures to speed such searches can greatly reduce the risk involved, increase the number of individuals whose remains are recovered and identified, and more importantly, reunite these remains with their loved ones to provide them with a proper burial. Geographic information systems (GIS) software, which can analyze and manipulate the spatial characteristics of known mass grave data, represents a powerful tool that can be used to predict new mass grave locations and increase the speed and efficiency with which they are investigated. Using the open source QGIS project, existing mass grave locations in Guatemala were analyzed based on their distance from and change in elevation relative to roads, streets, waterways, points of interest, and possible villages/towns. Statistical and geostatistical analyses performed to detect relationships among the variables resulted in patterns that warrant further study and can be used to further narrow areas of investigation.

Abstracting mobility flows from bike-sharing systems.

Bicycling has grown significantly in the past ten years. In some regions, the implementation of large-scale bike-sharing systems and improved cycling infrastructure are two of the factors enabling this growth. An increase in non-motorized modes of transportation makes our cities more human, decreases pollution, traffic, and improves quality of life. In many cities around the world, urban planners and policymakers are looking at cycling as a sustainable way of improving urban mobility. Although bike-sharing systems generate abundant data about their users' travel habits, most cities still rely on traditional tools and methods for planning and policy-making. Recent technological advances enable the collection and analysis of large amounts of data about urban mobility, which can serve as a solid basis for evidence-based policy-making. In this paper, we introduce a novel analytical method that can be used to process millions of bike-sharing trips and analyze bike-sharing mobility, abstracting relevant mobility flows across specific urban areas. Backed by a visualization platform, this method provides a comprehensive set of analytical tools to support public authorities in making data-driven policy and planning decisions. This paper illustrates the use of the method with a case study of the Greater Boston bike-sharing system and, as a result, presents new findings about that particular system. Finally, an assessment with expert users showed that this method and tool were considered very useful, relatively easy to use and that they intend to adopt the tool in the near future.