Design, Development and Application of a Modular Electromagnetic Induction (EMI) Sensor for Near-Surface Geophysical Surveys.

Low-frequency electromagnetic induction (EMI) is a non-invasive geophysical method that is based on the induction of electromagnetic (EM) waves into the subsurface to quantify changes in electrical conductivity. In this study, we present an open (design details and software are accessible) and modular system for the collection of EMI data. The instrument proposed allows for the separations between the transmitter to be adjusted and up to four receiving antennas as well as the acquisition frequency (in the range between 3 and 50 kHz) to permit measurements with variable depth of investigation. The sensor provides access to raw data and the software described in this study allows control of the signal processing chain. The design specifications permit apparent conductivity measurements in the range of between 1 mS/m and 1000 mS/m, with a resolution of 1.0 mS/m and with a sampling rate of up to 10 samples per second. The sensor allows for a synchronous acquisition of a time stamp and a location stamp for each data sample. The sensor has a mass of less than 5 kg, is portable and suitable for one-person operation, provides 4 h of operation time on one battery charge, and provides sufficient rigidity for practical field operations.

EnderScope: a low-cost 3D printer-based scanning microscope for microplastic detection.

Low-cost and scalable technologies that allow people to measure microplastics in their local environment could facilitate a greater understanding of the global problem of marine microplastic pollution. A typical way to measure marine microplastic pollution involves imaging filtered seawater samples stained with a fluorescent dye to aid in the detection of microplastics. Although traditional fluorescence microscopy allows these particles to be manually counted and detected, this is a resource- and labour-intensive task. Here, we describe a novel, low-cost microscope for automated scanning and detection of microplastics in filtered seawater samples-the EnderScope. This microscope is based on the mechanics of a low-cost 3D printer (Creality Ender 3). The hotend of the printer is replaced with an optics module, allowing for the reliable and calibrated motion system of the 3D printer to be used for automated scanning over a large area (>20 × 20 cm). The EnderScope is capable of both reflected light and fluorescence imaging. In both configurations, we aimed to make the design as simple and cost-effective as possible, for example, by using low-cost LEDs for illumination and lighting gels as emission filters. We believe this tool is a cost-effective solution for microplastic measurement. This article is part of the Theo Murphy meeting issue 'Open, reproducible hardware for microscopy'.

Optical projection tomography implemented for accessibility and low cost (OPTImAL).

Optical projection tomography (OPT) is a three-dimensional mesoscopic imaging modality that can use absorption or fluorescence contrast, and is widely applied to fixed and live samples in the mm-cm scale. For fluorescence OPT, we present OPT implemented for accessibility and low cost, an open-source research-grade implementation of modular OPT hardware and software that has been designed to be widely accessible by using low-cost components, including light-emitting diode (LED) excitation and cooled complementary metal-oxide-semiconductor (CMOS) cameras. Both the hardware and software are modular and flexible in their implementation, enabling rapid switching between sample size scales and supporting compressive sensing to reconstruct images from undersampled sparse OPT data, e.g. to facilitate rapid imaging with low photobleaching/phototoxicity. We also explore a simple implementation of focal scanning OPT to achieve higher resolution, which entails the use of a fan-beam geometry reconstruction method to account for variation in magnification. This article is part of the Theo Murphy meeting issue 'Open, reproducible hardware for microscopy'.

Arduino-Based Readout Electronics for Nuclear and Particle Physics.

Open Hardware-based microcontrollers, especially the Arduino platform, have become a comparably easy-to-use tool for rapid prototyping and implementing creative solutions. Such devices in combination with dedicated front-end electronics can offer low-cost alternatives for student projects, slow control and independently operating small-scale instrumentation. The capabilities can be extended to data taking and signal analysis at mid-level rates. Two detector realizations are presented, which cover the readouts of proportional counter tubes and of scintillators or wavelength-shifting fibers with silicon photomultipliers (SiPMs). The SiPMTrigger realizes a small-scale design for coincidence readout of SiPMs as a trigger or veto detector. It consists of a custom mixed signal front-end board featuring signal amplification, discrimination and a coincidence unit for rates of up to 200 kHz. The nCatcher transforms an Arduino Nano to a proportional counter readout with pulse shape analysis: time over threshold measurement and a 10-bit analog-to-digital converter for pulse heights. The device is suitable for low-to-medium-rate environments up to 5 kHz, where a good signal-to-noise ratio is crucial. We showcase the monitoring of thermal neutrons. For data taking and slow control, a logger board is presented that features an SD card and GSM/LoRa interface.

A Collaborative Platform for Advancing Automatic Interpretation in ECG Signals.

Numerous papers report the efficiency of the automatic interpretation capabilities of commercial algorithms. Unfortunately, these algorithms are proprietary, and academia has no means of directly contributing to these results. In fact, nothing at the same stage of development exists in academia. Despite the extensive research in ECG signal processing, from signal conditioning to expert systems, a cohesive single application for clinical use is not ready yet. This is due to a serious lack of coordination in the academic efforts, which involve not only algorithms for signal processing, but also the signal acquisition equipment itself. For instance, the different sampling rates and the different noise levels frequently found in the available signal databases can cause severe incompatibility problems when the integration of different algorithms is desired. Therefore, this work aims to solve this incompatibility problem by providing the academic community with a diagnostic-grade electrocardiograph. The intention is to create a new standardized ECG signals database in order to address the automatic interpretation problem and create an electrocardiography system that can fully assist clinical practitioners, as the proprietary systems do. Achieving this objective is expected through an open and coordinated collaboration platform for which a webpage has already been created.

Open continuum robotics-one actuation module to create them all.

Experiments on physical continuum robot are the gold standard for evaluations. Currently, as no commercial continuum robot platform is available, a large variety of early-stage prototypes exists. These prototypes are developed by individual research groups and are often used for a single publication. Thus, a significant amount of time is devoted to creating proprietary hardware and software hindering the development of a common platform, and shifting away scarce time and efforts from the main research challenges. We address this problem by proposing an open-source actuation module, which can be used to build different types of continuum robots. It consists of a high-torque brushless electric motor, a high resolution optical encoder, and a low-gear-ratio transmission. For this article, we create three different types of continuum robots. In addition, we illustrate, for the first time, that continuum robots built with our actuation module can proprioceptively detect external forces. Consequently, our approach opens untapped and under-investigated research directions related to the dynamics and advanced control of continuum robots, where sensing the generalized flow and effort is mandatory. Besides that, we democratize continuum robots research by providing open-source software and hardware with our initiative called the Open Continuum Robotics Project, to increase the accessibility and reproducibility of advanced methods.

MagnetoShield: A Novel Open-Source Magnetic Levitation Benchmark Device for Mechatronics Education and Research.

This article presents an open-source device illustrating the well-known magnetic levitation experiment. The uniqueness of this particular device lies in its exceptionally small dimensions, affordability and availability, which makes it a perfect design for take-home experiments for education but it can also serve as a referential design for testing various control algorithms in research. In addition, this paper provides a comprehensive hardware design for reproducibility along with the detailed derivation of the mathematical model, system identification and validation. Moreover, the introduced hardware comes with an easy-to-use open-source application programming interface in C/C++ for the Arduino IDE, Simulink and CircuitPython. REXYGEN, another environment similar to Simulink, had also been used to demonstrate the capabilities of the MagnetoShield.

Exploring pathways toward open-hardware ecosystems to safeguard genetic resources for biomedical research communities using aquatic model species.

Development of reliable germplasm repositories is critical for preservation of genetic resources of aquatic species, which are widely utilized to support biomedical innovation by providing a foundational source for naturally occurring variation and development of new variants through genetic manipulations. A significant barrier in repository development is the lack of cryopreservation capability and reproducibility across the research community, posing great risks of losing advances developed from billions of dollars of research investment. The emergence of open scientific hardware has fueled a new movement across biomedical research communities. With the increasing accessibility of consumer-level fabrication technologies, such as three-dimensional printers, open hardware devices can be custom designed, and design files distributed to community members for enhancing rigor, reproducibility, and standardization. The overall goal of this review is to explore pathways to create open-hardware ecosystems among the communities using aquatic model resources for biomedical research. To gain feedback and insights from community members, an interactive workshop focusing on open-hardware applications in germplasm repository development was held at the 2022 Aquatic Models for Human Disease Conference, Woods Hole, Massachusetts. This work integrates conceptual strategies with practical insights derived from workshop interactions using examples of germplasm repository development. These insights can be generalized for establishment of open-hardware ecosystems for a broad biomedical research community. The specific objectives were to: (1) introduce an open-hardware ecosystem concept to support biomedical research; (2) explore pathways toward open-hardware ecosystems through four major areas, and (3) identify opportunities and future directions.

RPM: An open-source Rotation Platform for open- and closed-loop vestibular stimulation in head-fixed Mice.

Head fixation allows the recording and presentation of controlled stimuli and is used to study neural processes underlying spatial navigation. However, it disrupts the head direction system because of the lack of vestibular stimulation. To overcome this limitation, we developed a novel rotation platform which can be driven by the experimenter (open-loop) or by animal movement (closed-loop). The platform is modular, affordable, easy to build and open source. Additional modules presented here include cameras for monitoring eye movements, visual virtual reality, and a micro-manipulator for positioning various probes for recording or optical interference. We demonstrate the utility of the platform by recording eye movements and showing the robust activation of head-direction cells. This novel experimental apparatus combines the advantages of head fixation and intact vestibular activity in the horizontal plane. The open-loop mode can be used to study e.g., vestibular sensory representation and processing, while the closed-loop mode allows animals to navigate in rotational space, providing a better substrate for 2-D navigation in virtual environments. The full build documentation is maintained at https://ranczlab.github.io/RPM/.

Open Hardware Implementation of Real-Time Phase and Amplitude Estimation for Neurophysiologic Signals.

Adaptive deep brain stimulation (aDBS) is a promising concept in the field of DBS that consists of delivering electrical stimulation in response to specific events. Dynamic adaptivity arises when stimulation targets dynamically changing states, which often calls for a reliable and fast causal estimation of the phase and amplitude of the signals. Here, we present an open-hardware implementation that exploits the concepts of resonators and Hilbert filters embedded in an open-hardware platform. To emulate real-world scenarios, we built a hardware setup that included a system to replay and process different types of physiological signals and test the accuracy of the instantaneous phase and amplitude estimates. The results show that the system can provide a precise and reliable estimation of the phase even in the challenging scenario of dealing with high-frequency oscillations (~250 Hz) in real-time. The framework might be adopted in neuromodulation studies to quickly test biomarkers in clinical and preclinical settings, supporting the advancement of aDBS.

OptoPi: An open source flexible platform for the analysis of small animal behaviour.

Behaviour is the ultimate output of neural circuit computations, and therefore its analysis is a cornerstone of neuroscience research. However, every animal and experimental paradigm requires different illumination conditions to capture and, in some cases, manipulate specific behavioural features. This means that researchers often develop, from scratch, their own solutions and experimental set-ups. Here, we present OptoPi, an open source, affordable (∼ £600), behavioural arena with accompanying multi-animal tracking software. The system features highly customisable and reproducible visible and infrared illumination and allows for optogenetic stimulation. OptoPi acquires images using a Raspberry Pi camera, features motorised LED-based illumination, Arduino control, as well as irradiance monitoring to fine-tune illumination conditions with real time feedback. Our open-source software (BioImageProcessing) can be used to simultaneously track multiple unmarked animals both in on-line and off-line modes. We demonstrate the functionality of OptoPi by recording and tracking under different illumination conditions the spontaneous behaviour of larval zebrafish as well as adult Drosophila flies and their first instar larvae, an experimental animal that due to its small size and transparency has classically been hard to track. Further, we showcase OptoPi's optogenetic capabilities through a series of experiments using transgenic Drosophila larvae.

Open source scientific bottle roller.

Proprietary bottle rolling systems automate some laboratory applications, however, their high costs limit accessibility. This study provides designs of an open source bottle roller that is compatible with distributed digital manufacturing using 3-D printed parts and readily-available commercial components. The experimental results show that the open source bottle roller can be fabricated for CAD$210 (about USD$150) in materials, which is 86% less expensive than the most affordable proprietary bottle roller on the market. The design, however, is more robust with enhanced capabilities. The design can be adapted to the user's needs, but is already compatible with incubators with a low profile (dimensions 50 cm x46 cm x8.8 cm) and capable of being operated at elevated temperatures. The systems can be adjusted to revolves from 1 to 200 RPM, exceeding the rotational speed of most commercial systems. The open source bottle roller as tested has a capacity greater than 1.2 kg and can roll twelve 100 mL bottles simultaneously. Validation testing showed that it can operate for days at 80 RPM without human intervention or monitoring for days at both room temperature and elevated temperatures (50 °C). Future work includes adapting the designs for different sizes and for different fabrication techniques to further reduce costs and increase flexibility.

Open hardware in microscopy.

The field of microscopy has been empowering humankind for many centuries by enabling the observation of objects that are otherwise too small to detect for the naked human eye. Microscopy techniques can be loosely divided into three main branches, namely photon-based optical microscopy, electron microscopy, and scanning probe microscopy with optical microscopy being the most prominent one. On the high-end level, optical microscopy nowadays enables nanometer resolution covering many scientific disciplines ranging from material sciences over the natural sciences and life sciences to the food sciences. On the lower-end level, simplified hardware and openly available description and blueprints have helped to make powerful microscopes widely available to interested scientists and researchers. For this special issue, we invited contributions from the community to share their latest ideas, designs, and research results on open-source hardware in microscopy. With this collection of articles, we hope to inspire the community to further increase the accessibility, interoperability, and reproducibility of microscopy. We further touch on the standardization of methodologies and devices including the use of computerized control of data acquisition and data analysis to achieve high quality and efficiency in research and development.

A Low-Cost Radar-Based IoT Sensor for Noncontact Measurements of Water Surface Velocity and Depth.

We designed an out-of-water radar water velocity and depth sensor, which is unique due to its low cost and low power consumption. The sensor is a first at a cost of less than USD 50, which is well suited to previously cost-prohibited high-resolution monitoring schemes. This use case is further supported by its out-of-water operation, which provides low-effort installations and longer maintenance-free intervals when compared with in-water sensors. The inclusion of both velocity and depth measurement capabilities allows the sensor to also be used as an all-in-one solution for flowrate measurement. We discuss the design of the sensor, which has been made freely available under open-hardware and open-source licenses. The design uses commonly available electronic components, and a 3D-printed casing makes the design easy to replicate and modify. Not before seen on a hydrology sensor, we include a 3D-printed radar lens in the casing, which boosts radar sensitivity by 21 dB. The velocity and depth-sensing performance were characterised in laboratory and in-field tests. The depth is accurate to within ±6% and ±7 mm and the uncertainty in the velocity measurements ranges from less than 30% to 36% in both laboratory and field conditions. Our sensor is demonstrated to be a feasible low-cost design which nears the uncertainty of current, yet more expensive, velocity sensors, especially when field performance is considered.

Distributed manufacturing of an open-source tourniquet testing system.

Tourniquets are effective for casualty-prevention in emergency situations. The use of centrally-manufactured commercial tourniquets, however, is not always possible due to supply chain disruptions. The open-source hardware model has been applied to overcome these disruptions in humanitarian crises and several low-cost digitally manufacturable open-source tourniquets have been developed. With the low reliability of improvised tourniquets, it is important to ensure that distributed manufacturing of tourniquets is effective and safe. Tourniquets can be tested, but existing tourniquet testers are expensive, bulky, and complex to operate, which limits their accessibility to an even greater extent than tourniquets in extreme settings. This article fulfills a need by providing a small, transportable, open-source additive-manufactured tourniquet tester that enables inexpensive and accurate testing of tourniquets against known clinical parameters. The <$100 tourniquet tester is validated and tested for operating force of tourniquets in the field or in distributed manufacturing facilities. The tourniquet tester has a significant economic and operational advantage compared to proprietary counterparts available on the market. Once calibrated with a blood pressure monitor, the built-in LCD displays the measuring range of the tester as 0 to 200 N, which is enough to test the validation of all tourniquets.

Versatile open-source fluorescence documentation system.

Fluorescence has long been the best method for detecting bio-molecules at high sensitivity and with the possibility of easy data analysis and is routine for gel electrophoresis and much more. However, the systems for detecting the fluorophores remain expensive and thus inaccessible to many. Most commercial systems are often only optimized for one specific application, making reuse difficult. This paper demonstrates, characterizes and evaluates an inexpensive and versatile system for the detection of fluorophores with two wavelengths using high power LEDs. The LEDs are arranged in two banks angled downward at a tray in a way that allows for bright and uniform illumination while preventing direct reflections into the camera. The emitted light is filtered through an exchangeable filter frame and can be detected using the camera of a smartphone or similar device. By using filters both in front of the LEDs and the camera, very low background and using sufficient exposure times, very high sensitivity can be achieved. The two wavelengths of excitation light and the exchangeable filters allow for optimization for the specific fluorophore used and thus highest brightness.

Arduino based intra-cerebral microinjector device for neuroscience research.

Stereotaxic surgery is a less invasive form of surgery that uses a three-dimensional coordinate system to place instruments at a specific location in the brain. Through this type of surgery, one can place needles among other tools within the structures of the brain. Therefore, injections can be given in order to deliver substances that cannot cross the blood-brain barrier. The two most important parameters of the microinjection to control are volume and speed. The volume should not be so large that it displaces the brain tissue and tears it. The injection speed must also be slow so that the liquid that comes out of the syringe can diffuse into the tissue without displacing it and damaging it. Thus, the objectives of the present work are: 1) To develop not a 3D printed prototype but an end-user device. 2) The device must be for animal research only. 3) It must have the same precision in volume and speed as commercial devices. 4) It must be adjustable for microsyringes from 0.5 µl to 1 ml. 5) It must be possible to place it directly on the stereotaxic surgery apparatus and to use it separately. 6) The price must be substantially lower than that of the commercial devices.

Zoobooth: A portable, open-source and affordable approach for repeated size measurements of live individual zooplankton.

Repeated size measurements of individual animals are valuable data for many research questions, but it is often hard to obtain without causing stress or damage to the animal. We developed a video-based approach called Zoobooth to size individual zooplankton, which involves a low risk of handling accidents and stress. Here we describe the process of assembling the instrument we used to acquire video recordings of single zooplankton and the procedure to obtain size estimates from the recorded videos. Our setup produces accurate size estimates for Daphnia magna (correlation to manual measurements = 0.97), and was also tested with other zooplankton species. Zoobooth is especially advantageous when one needs size measurements of live, individual mesozooplankton. The device is small, portable, and comprised of very affordable and readily available components. It can easily be modified for other purposes, such as studies of coloration or behavior of micro-and macro-plankton. We share all the files to build and use Zoobooth.

AC/off-grid photovoltaic powered open-source ball mill.

Ball milling is used for comminution by rotating a drum to grind materials using balls with specific diameters. Ball milling advantages include the potential for high capacity, predicted fineness in a specific amount of time, reliability, safety, and simplicity, but has disadvantages of high weight, energy consumption and costs, which limit accessibility. To overcome these limitations this study applies the free and open source hardware approach coupled to distributed digital manufacturing to fabricate a ball mill with a simple, customizable design that can be used in a wide range of scientific applications and circumstances including those without access to reliable grid electricity. The highly-customizable design reduces the cost to

Hangprinter for large scale additive manufacturing using fused particle fabrication with recycled plastic and continuous feeding.

The life cycle of plastic is a key source of carbon emissions. Yet, global plastics production has quadrupled in 40 years and only 9 % has been recycled. If these trends continue, carbon emissions from plastic wastes would reach 15 % of global carbon budgets by 2050. An approach to reducing plastic waste is to use distributed recycling for additive manufacturing (DRAM) where virgin plastic products are replaced by locally manufactured recycled plastic products that have no transportation-related carbon emissions. Unfortunately, the design of most 3-D printers forces an increase in the machine cost to expand for recycling plastic at scale. Recently, a fused granular fabrication (FGF)/fused particle fabrication (FPF) large-scale printer was demonstrated with a GigabotX extruder based on the open source cable driven Hangprinter concept. To further improve that system, here a lower-cost recyclebot direct waste plastic extruder is demonstrated and the full designs, assembly and operation are detailed. The <$1,700 machine's accuracy and printing performance are quantified, and the printed parts mechanical strength is within the range of other systems. Along with support from the Hangprinter and DUET3 communities, open hardware developers have a rich ecosystem to modify in order to print directly from waste plastic for DRAM.