HardwareX

Measuring optical density (OD) is a very common technique in biological laboratories to determine the concentration of a substance in solution or of bacteria (or microscopic particles) in suspension. For example, bacterial cultures engineered to produce (express) a protein or compound of interest are a workhorse of modern molecular biology laboratories. Commonly, the expression of the product is triggered (induced) by a chemical signal added to the culture at the proper time in the growth curve of the culture (typically in the middle of the exponential growth phase, at an OD value of [~]0.6). The most common tool for measuring OD is a spectrophotometer. However, most spectrophotometers are sophisticated, non-portable and expensive laboratory instruments, costing tens of thousands of dollars. Even a very low cost spectrophotometer for educational use costs at least US$1,000. Because of the cost, even well resourced labs have only one instrument, which becomes a bottleneck when multiple bacterial cultures need to be monitored simultaneously. The problem is more acute in developing countries, where multiple labs have to share a single spectrophotometer, or theres no such instrument at all. Having a cheap and simple device to measure OD would enable multiple people in a laboratory to monitor their bacterial cultures independently, even in resource-limited settings. At the same time, a portable OD meter could be useful for field work. Here we present the detailed build instructions and characterization of a very simple OD meter that costs only US$60, and can measure OD values from [~]0.05 to 2.0. Specifications table O_TBL View this table: org.highwire.dtl.DTLVardef@721005org.highwire.dtl.DTLVardef@79c5d3org.highwire.dtl.DTLVardef@aabb95org.highwire.dtl.DTLVardef@1016f09org.highwire.dtl.DTLVardef@120f3e2_HPS_FORMAT_FIGEXP M_TBL C_TBL

A very large number of biology and biochemistry laboratory protocols require transferring liquid aliquots from individual containers into individual wells of a multi-well plate, from plates to individual containers, or from one plate to another. Doing this by hand without errors, such as skipping wells, placing two samples in the same well, or swapping sample locations, especially when using plates with 96 wells or more, is difficult and requires enormous operator focus and/or a tedious manual error checking system. We present here a device built to facilitate error-free pipetting of samples from individual barcoded tubes to a multi-well plate or between multi-well plates (both 96 and 384 wells are supported). The device is programmable, modular and easily customizable to accommodate plates with different form-factors, and different protocols. The main components are only a 12.3" touch screen, a small form-factor PC, and a barcode scanner, combined with custom-made parts can be easily fabricated with a laser cutter and a hobby-grade 3D printer. The total cost is between approximately US$550 and US$600, depending on the configuration. Specifications table O_TBL View this table: org.highwire.dtl.DTLVardef@8554f4org.highwire.dtl.DTLVardef@18c8878org.highwire.dtl.DTLVardef@153b050org.highwire.dtl.DTLVardef@15c7de6org.highwire.dtl.DTLVardef@14daeb7_HPS_FORMAT_FIGEXP M_TBL C_TBL

Rodent mazes have been used for decades to study the neural basis of behavior. Advancements in rapid prototyping techniques and access to affordable electronics allows laboratories with sufficient expertise in engineering and programming to customize and construct maze apparatuses and behavioral tasks, thereby increasing the ability of their studies to answer specific scientific questions. We designed and built a rodent gate system that lowers this bar of expertise even further. The NC4gate system is a robust mechanical design that can be built using low-cost hardware and execute thousands of cycles before maintenance. Up to 512 gates can be controlled using a single computer. Users can control the gates interactively using a Python-based graphical interface and programmatically using an extensible API. We hope that the open-source hardware / software and extensive documentation enables laboratories to build these affordable and robust gates and seamlessly incorporate automatic behavior control into their existing or new rodent tasks. Significance StatementRodent mazes are used by thousands of laboratories and research institutions across the world to study learning and memory, as well as the effects of pharmacological, genetic and environmental manipulations. Ideally, maze and task designs should be customized to the scientific questions at hand. It is challenging, however, for many laboratories to build, program, and operate custom mazes, requiring them instead to rely on expensive and proprietary commercial solutions. The most complex components of most mazes are moving gates that restrict and direct rodent behavior. Here we provide the open-source hardware and software for a gate system that is extensible, affordable and robust, removing this critical barrier to customized mazes.

The BIO-SPEC is an open-source, cost-effective, and modular bench-top bioreactor system designed for batch, sequencing batch, and chemostat cultivation. Featuring thermoelectric condensers to eliminate the need for a chiller, it ensures stable long-term operation. Controlled by a Raspberry Pi, the BIO-SPEC offers flexibility in headplate design, gas supply, and feeding strategies, making it a versatile alternative to high-cost commercial systems. This paper details the design, construction, and validation of the BIO-SPEC system, demonstrating its potential to advance microbiology and bioprocessing research through accessible and reliable hardware at a fraction of the cost.

High-resolution in vivo microscopy approaches can reveal subtle information and fine details inside the model animal Caenorhabditis elegans (C. elegans) but requires strong animal immobilization. Unfortunately, most current immobilization techniques require substantial manual effort, rendering high-resolution imaging low-throughput. We greatly simplify the C. elegans immobilization procedure by using a cooling approach that can easily immobilize entire populations of C. elegans directly on their cultivation plates. The cooling stage can establish and maintain a wide range of temperatures on the cultivation plate and ensures even temperature distribution across the agarose surface. In this article, we document the whole process of building the cooling stage from scratch. We envision that a typical researcher can build an operational cooling stage in their lab following our protocol without difficulty. We show how to utilize the cooling stage under three protocols, which have advantages for different experiments. We also show an example cooling profile of the stage as it approaches its final temperature and include some helpful tips in using cooling immobilization.

Live imaging of human or other mammalian cells at multi-hour time scales with minimal perturbation to their growth state requires that the specimens optimal growth conditions are met while fixed to a microscope stage. In general, ideal conditions include culturing in complete growth media, an ambient temperature of 36-37 C, and a humidity-controlled atmosphere comprising typically 5-7% CO2. Commercially available devices that achieve these conditions are not a financially viable option for many labs, with the price ranging anywhere from $12000 to $40000. The advent of 3D printing technology has allowed for low-cost rapid prototyping with precision comparable to traditional fabrication methods, opening the possibility for in-lab design and production of otherwise prohibitively expensive equipment such as stage-top incubation devices. The continued usefulness and widespread availability of single-board computers (SBC) such as Arduino and Raspberry Pi also simplify the process by which these devices can be controlled. Here we report the production of a do-it-yourself (DIY) device for stage-top incubation with temperature and atmospheric control with a cost reduction of approximately 100x.

1Isothermal amplification-based methods for pathogen DNA or RNA detection offer high sensitivity, rapid detection, and the potential for deployment in remote fields and home testing. Consequently, they are emerging as alternatives to PCR and saw a surge in research activity and deployment for the rapid detection of SARS-CoV-2 during the Covid-19 pandemic. The most common isothermal DNA detection methods rely on minimal reagents for DNA amplification and simple hardware that can maintain isothermal conditions and read-out a fluorescent or colorimetric signal. Many researchers globally are working on improving these components based on diverse end-user needs. In this work, we have recognized the need for an open-source hardware device for isothermal amplification, composed of off-the-shelf components that are easily accessible in any part of the world, is easily manufacturable in a distributed and scalable way using 3D printing, and that can be powered using a wide diversity of batteries and power sources. We demonstrate the easy assembly of our device design and demonstrate its efficacy using colorimetric LAMP for both RNA and DNA targets.

Modern data analysis methods, such as optimisation algorithms or machine and deep learning, have been successfully applied to a number of biological, biotechnological and medical questions. For these methods to be efficient, a large number of high quality experiments need to be conducted, which requires a high degree of automation. Here we report an open-source hardware that allows for automatic high-throughput generation of large amounts of cell biology data. The hardware consists of an automatic XY-stage for moving a multiwell plate containing growing cells; a perfusion manifold allowing application of up to 8 different solutions; and a small epifluorescent microscope. It is extremely cheap (approximately {pound}400 without and {pound}2500 with a fluorescent microscope) and is easily customizable for individual experimental needs. We demonstrate the usability of this platform with high-throughput Ca2+ imaging and large-scale labelling experiments. Key points- We present an open source framework for automation of cell biology experiments - The framework consists of an XY platform, application of up to 8 solutions and a small epifluorescent microscope with autofocusing - Very cheap ({pound}400 without a fluorescent microscope and {pound}2500 with a fluorescent microscope), customisable, - Can be used in a variety of biological applications such as imaging of fluorescent reporters, optimisation of treatment conditions and fluorescent labelling

Several different types of open source feeders have been used in animal experiments in cognitive biology, neuroscience, psychology and related fields. These feeders use either dry pellets, which have hard surface and simple shape, or liquid food types such as sucrose solution. These food types can be rather easily manipulated due to its physical attributes. Although it is beneficial in terms of controllability, animal subjects often lose motivation to interact with operant conditioning devices offering such food items. Using natural food items such as fruits, insects, worms and pieces of meat will be helpful to keep the subjects motivation high, however, those food items are not very well suited for currently available open source feeders due to its physical attributes, including its complex shape, sticky and delicate texture. We made a feeder to deliver such natural food items to animal subjects for operant conditioning, using relatively cheap and easily obtainable parts. For a validation, we built a full operant conditioning device for wolves and dogs, containing two of these feeders, a pressure-sensitive monitor and a speaker.\n\nSpecifications table\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@f65995org.highwire.dtl.DTLVardef@1736cacorg.highwire.dtl.DTLVardef@e3b1c6org.highwire.dtl.DTLVardef@ac3e9eorg.highwire.dtl.DTLVardef@432ab4_HPS_FORMAT_FIGEXP M_TBL C_TBL

Live-cell microscopy imaging typically involves the use of high-quality glass-bottom chambers that allow cell culture, gaseous buffer exchange and optical properties suitable for microscopy applications. However, commercial sources of these chambers can add significant annual costs to cell biology laboratories. Consumer products in three-dimensional printing technology, for both Filament Deposition Modeling (FDM) and Masked Stereo Lithography (MSLA), have resulted in more biomedical research labs adopting the use of these devices for prototyping and manufacturing of lab plastic-based items, but rarely consumables. Here we describe a modular, live-cell chamber with multiple design options that can be mixed per experiment. Single reusable carriers and the use of biodegradable plastics, in a hybrid of FDM and MSLA manufacturing methods, reduce plastic waste. The system is easy to adapt to bespoke designs, with concept-to-prototype in a single day, offers significant cost savings to the users over commercial sources, and no loss in dimensional quality or reliability.

Laboratory automation can greatly accelerate experiments and data collection, yet building automated systems often requires substantial programming and electronics expertise, and few frameworks are targeted at deploying many devices. We present LAS3R, a low-cost, open-source framework that enables researchers with minimal technical expertise to rapidly prototype, deploy, remotely control, and collect data from multiple custom-built laboratory devices while maintaining strong security and reliability throughout the process--from early prototyping to routine operation. The system is built around a central hub to which multiple lab devices connect. This hub can be set up on a Raspberry Pi (a small, low-cost single-board computer) in under fifteen minutes. In the setup process, code is automatically generated for ESP32 microcontroller boards that control the hardware. Users can choose from a list of preconfigured ESP32 devices, for example a bioreactor, or use a template that provides base code for many common automation tasks, which they can then easily customise using the beginner-friendly Arduino platform. The ESP32 devices connect through a secure Wi-Fi network hosted by the Raspberry Pi that encrypts communication, and ensures only authorised hardware can join, helping safeguard experimental data and institutional networks, even while prototyping. We demonstrate the framework with two applications--a turbidostat bioreactor and a light-level controller--and show that it can simultaneously manage eight devices with 24 sensors. Robustness was evaluated through single-point-of-failure analysis, confirming continued operation during mains power or network interruptions. Comprehensive documentation, aimed at wet lab researchers, enables users to understand, build, and adapt the system, making it both a practical laboratory automation platform, including for those in low-resource settings, and a teaching resource. This paper is intended to be a technical evaluation of the architecture. Those wishing to deploy the system should refer to the online documentation at kavihshah.github.io/LAS3R.

This work presents the design and fabrication of MAIA, an open-source, modular, low-cost, and portable bioreactor for democratizing the development of synthetic biology based projects for urban settings. The integration of open-source synthetic biology (synbio) tools in a citys infrastructure planning and design is crucial for addressing the great challenges related to urbanization. Synbio tools have great potential to help us complement our current sensing and actuating urban infrastructure. The MAIA reactor controls bacterial growth variables, making it suitable for cell-based experiments while reducing the need for expensive laboratory equipment. Its low-cost and open-source design allow for easy replication and modification, making it accessible to a broader audience. Its portability makes it suitable for use outside of traditional laboratory settings. We qualitatively and quantitatively validated the reactors capability to support cell growth, stimulate gene expression, and act as a creative tool for students and users.

Experiments with biological samples require precise control of environmental conditions. In our work we use zebrafish (Danio rerio) to understand the neurobiology of sleep, which requires precise control of temperature and lighting. Like many labs, lighting and temperature in the animal facility are centrally controlled in the building. During behavioral experiments and microscopy sessions, we use custom-built heating systems and perform occasional manual checks of conditions. However, without a system to precisely record conditions, gradual changes in temperature can go unnoticed for a long time, and temporary failures may be missed entirely. Here we present the design and characterization of affordable open-source tools to record temperature and light conditions during animal experiments using an Arduino microcontroller or a Raspberry Pi compact computer. The waterproof temperature sensor has high stability over 50 days of recording and is precise to 0.1{degrees}C. The Arduino device can be used through a common serial port interface for which we present code in Python and MATLAB. The Raspberry Pi version can be accessed through a web interface, for which we provide an installation guide. We use the device to record and review temperature and lighting conditions in two zebrafish animal facilities. We use our platform to add a water heating system to maintain temperature at 28{degrees}C during in vivo light-sheet imaging of larval zebrafish. We show that a change in temperature from 28{degrees}C to 32{degrees}C affects resting heart rate of the animal, highlighting the importance of maintaining and recording conditions. The protocols presented here do not require advanced engineering, fabrication, or software skills, and provide an approach to accurately record and report experimental conditions.

Fluorescent time-lapse experiments often suffer from focus drift, regularly rendering long measurements partially unusable. Frequently, this instability can be traced back to the specific mechanical components of the setup, but even in highly robust implementations z-drift occurs due to small temperature fluctuations which are hard to avoid. To resolve this issue, microscope manufacturers often offer their own interpretation of out-of-focus correction modules for their flagship instruments. However, self-assembled or older systems typically have to fend for their own or adapt their measurements to circumvent drift effects. In this manuscript, we propose a cost-efficient z-drift detection- and correction system that, due to its modular design, can be attached to any fluorescence microscope with an actuated stage or objective, be it in a custom or commercial setup. The reason for this wide applicability is specific to the design, which has a straightforward alignment procedure and allows sharing optics with the fluorescent emission path. Our system employs an infrared (IR) laser that is passed through a double-hole mask to achieve two parallel beams which are made to reflect on the coverslip and subsequently detected on an industrial sCMOS camera. The relative position of these beams is then uniquely linked to the z-position of a microscope-mounted sample. The system was benchmarked by introducing temperature perturbations, where it was shown to achieve a stable focus, and by scanning different positions while simulating a perturbation in the z-position of the stage, where we show that a lost focus can be recovered within seconds.

Operant animal behavior training and monitoring is fundamental to scientific inquiry across fields necessitating evaluation via controlled laboratory tasks. However, current commercial and open-source systems enforce particular hardware and software, limiting reproducibility and technique and data sharing across sites. To address this issue, we developed OSCAR: an open-source controller for animal research that enables flexible control of a variety of industry standard hardware with platform-independent software. OSCAR offers millisecond latency with a flexible array of inputs and outputs at a fraction of the cost of commercial options. These features position OSCAR as a valuable option for improving consistency of behavioral experiments across studies.

Current myopia research has demonstrated the role of extended visual experience in healthy ocular development. Optical cues and the spectrum, intensity, and temporal characteristics of light landing on the retina are all known factors affecting the development of the eye. However, there is still limited understanding as to which of these extrinsic factors are most important or how they interplay with intrinsic physical and neural differences between individuals. Part of the problem is inadequate tooling. Our team at Reality Labs Research created the Visual Environment Evaluation Tool (VEET), a non-commercial research instrument, to accelerate myopia research. In this paper, we describe the VEETs physical design, sensor suite and capabilities, and the associated software which makes it well-suited for research of quantified visual experience.

The expanding scope of laboratory automation increasingly demands systems that can be tailored to specific experimental constraints, including footprint, timing, cost, and control. While open-source software has improved protocol flexibility, liquid-handling hardware itself remains largely closed, limiting the ability of academic and startup laboratories to build instruments around biological requirements rather than vendor defaults. Here, we present a fully open-source, purpose-built liquid-handling robot assembled from commercially available components and developed entirely in a research setting. The platform integrates open hardware, electronics, and a Python-based control stack compatible with PyLabRobot, exposing low-level motion dynamics and liquid-handling behaviors directly to experiment code. We validate the system using a high-throughput turbidostat workflow that requires rapid, closed-loop measurement and actuation to maintain microbial cultures at defined density setpoints. The robot sustains stable steady-state growth across approximately 200 cultures with heterogeneous growth dynamics. A replica build completed by two lab members in approximately one week confirms that the platform can be reproduced from its bill of materials and assembly guide. Its compact footprint and use of off-the-shelf components make it suitable for rapid, parallel deployment in settings such as public health emergencies or by distributed laboratories. Together, these results demonstrate that industry-class liquid handlers can be custom-built for specific experimental goals, establishing a blueprint for open, purpose-driven hardware development across research and industrial automation contexts. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=132 SRC="FIGDIR/small/709168v1_ufig1.gif" ALT="Figure 1"> View larger version (63K): org.highwire.dtl.DTLVardef@1b2cb4eorg.highwire.dtl.DTLVardef@1418e8dorg.highwire.dtl.DTLVardef@f60618org.highwire.dtl.DTLVardef@a3d3b_HPS_FORMAT_FIGEXP M_FIG Open Liquid Handler (OLH) Design Goals. Left: Design goals for a purpose-built platform for time-sensitive, closed-loop biological workflows, emphasizing high-accuracy dosing (low variability liquid handling), rapid integrated measurement (plate deck and isolated workspace), customizable deck and peripheral options, compact footprint with high throughput, containment via an enclosed wet workspace for biosafety and sterility, and a replicable build using off-the-shelf OEM components with open design files. Right: Open Liquid Handler design and physical implementation, with aerial and front views highlighting the enclosed cabinet and the working envelope over a compact deck. C_FIG

Multiomics studies at single-cell level require small volume manipulation, high throughput analysis and multiplexed detection, characteristics that droplet microfluidics can tackle. However, the initial step of molecules bioseparation remains challenging. Here, we describe a unique magnetic device to trap and extract magnetic particles in sub-nanoliter droplets, for compartmentalisation of detection steps. Relying on electrodeposition of NiFe structures and microfluidic manipulation, this technology has allowed the purification of genetic material at single-cell scale and was able to reach an extraction rate of 72% for a sample of purified oligonucleotides.

Planktonic organisms are a cornerstone of marine ecosystems. They vary significantly in size and have a repertoire of behaviors to aid them to survive and navigate their three-dimensional environment. One of the most important cues is light. A variety of setups were used to study the swimming behavior of specific organisms, but broader and comparative investigations need more versatile solutions. With the help of 3D printing, we designed and constructed a modular and flexible behavioral observation setup that enables recordings of animals down to 50m or up to a few centimeters. A video analysis pipeline using ImageJ and python allows a quick, automated, and robust tracking solution, capable of processing many videos automatically. A modular light path allows the addition of filters or use of pulse width modulation to equalize photon emission of LEDs or additional LEDs to mix different wavelengths. Optionally, a spectrometer can be installed to enable live monitoring of a stimulus. We tested the setup with two phototactic marine planktonic larvae. First, we investigated the spectral sensitivity of the 7-day old larvae of the polychaete Malacoceros fuliginosus and second, the behavior of the 200m spherical bryozoan coronated larvae of Tricellaria inopinata to ultraviolet light coming from the bottom of the vessel. The setup and pipeline were able to record and analyze hundreds of animals simultaneously. We present an inexpensive, modular, and flexible setup to study planktonic behavior of a variety of sizes.

Distributed "Point-of-Care" or "at-Home" testing is an important component for a complete suite of testing solutions. This manuscript describes the construction and operation of a platform technology designed to meet this need. The ongoing COVID-19 pandemic will be used as the proof-of-concept for the efficacy and deployment of this platform. The technology outlined consists of a one-pot, reverse-transcription loop-mediated isothermal amplification (RT-LAMP) chemistry coupled with a low-cost and user-assembled reader using saliva as input. This platform is readily adapted to a wide range of pathogens due to the genetic basis of the reaction. A complete guide to the construction of the reader as well as the production of the reaction chemistry are provided here. Additionally, analytical limit of detection data and the results from saliva testing of SARS-CoV-2, are presented. The platform technology outlined here demonstrates a rapid, distributed, molecular point-of-care solution for pathogen detection using crude sample input.