OpenWorkstation: A modular open-source technology for automated in vitro workflows

How to convert a 3D printer to a personal automated liquid handler for life science workflows

Automated liquid handlers are fundamental in modern life science laboratories, yet their high costs and large footprints often limit accessibility for smaller labs. This study presents an innovative approach to decentralizing a liquid handling system by converting a low-cost 3D printer into a customizable and accurate liquid handler. The Personal Automated Liquid Handler (PALH) system, costing ∼$400, incorporates a single-channel pipet, custom 3D-printed components, and open-source software for personalized workflows, allowing researchers to build and modify the system for specific experimental needs. The PALH system was evaluated through common life science assays, including preparing real-time PCR samples, end-point PCR with novel pipet-based downstream purification, and genomic DNA extraction from peripheral whole blood. In real-time PCR experiments targeting the YWHAZ gene, the PALH system demonstrated comparable performance to manual preparation across DNA quantities (1 pg to 100 ng). For end-point PCR, the PALH successfully amplified and purified 204 bp and 406 bp amplicons from a pUC19 vector, yielding concentrations similar to manual methods (5.43 ± 0.85 ng/µL vs. 2.10 ± 0.16 ng/µL for 204 bp; 3.74 ± 2.13 ng/µL vs. 1.51 ± 0.15 ng/µL for 406 bp, respectively). In genomic DNA extraction from whole blood, the PALH system achieved comparable DNA yields to manual extraction (49.52 ± 3.13 ng/µL vs. 48.62 ± 5.9 ng/µL), although at higher purity (260/280 ratio of 1.83 ± 0.07 vs. 1.92 ± 0.03), although both are at acceptable ranges. The open-source nature of the PALH system hopefully encourages further community-driven improvements and protocol sharing, fostering innovation and collaboration within the scientific community. As laboratory automation advances, the PALH system could be crucial in democratizing access to high-quality automated liquid handling, particularly in resource-limited settings.

Development of a digital amplifier system for cut-open oocyte electrophysiology

The cut-open oocyte Vaseline gap technique is a powerful electrophysiological method for the characterization of ion channels. However, traditional amplifiers for cut-open oocyte Vaseline gap are labor intensive and require significant user expertise. We introduce an innovative, open-source digital amplifier system with high-speed digitization and software-controlled electronics for computer-driven automation. This system compares well to existing commercial systems in terms of conventional specifications of step response (current peak at 25μs and decay of 36μs time constant), current noise (1.0 nA at 3-kHz bandwidth), and dynamic range (96.9 dB). Additionally, it unlocks new methods through close integration of the amplifier and software, including machine-learning techniques for tuning capacitive compensation waveforms, achieving a 100-fold suppression of mean-squared transient current, and impedance measurement methods to identify system components such as membrane capacitance and electrode resistances. For future extensions, the design has unique attributes such as real-time digital signal processing for feedback, multiple input and multiple output, and allows for user customization. By providing open-source access to the circuit board designs, control software, and field-programmable gate array code on GitHub, this approach aims to foster cross-disciplinary collaboration and facilitate instrument customization enabling previously inaccessible electrophysiology experiments.

Automation of multiplex biochemical assays to enhance productivity and reduce cycle time using a modular robotic platform

Pharmaceutical and biotechnology companies are increasingly being challenged to shorten the cycle time between design, make, test, and analyze (DMTA) compounds. Automation of multiplex assays to obtain multiparameter data on the same robotic run is instrumental in reducing cycle time. Consequently, an increasing need in automated systems to streamline laboratory workflows with the goal to expedite assay cycle time and enhance productivity has grown in industrial and academic institutions in the past decades. Herein, we present a customized robotic platform with operational modularity and flexibility, designed to automate entire assay workflows involving multistep reagent dispensing, mixing, lidding/de-lidding, incubation, centrifugation, and final readout steps by linking spinnaker robot with various peripheral instruments. Compared to manual workflows, the system can seamlessly execute processes with high efficiency, evaluated by standard assay validation protocols for robustness and reproducibility. Furthermore, the system can perform multiple, independent protocols in parallel, and has high-throughput capacity. In this publication, we demonstrate that the modular robotic platform can fully automate multiplex assay workflows through 'one-click-and-run' solution with tremendous benefits in liberating manual intervention, boosting productivity while producing high-quality data combined with reduced cycle time (>20 %), as well as expanding the capacity for higher throughput.

Automation of 3D digital rolling circle amplification using a 3D-printed liquid handler

Automation of liquid handling is indispensable to improve throughput and reproducibility in biochemical assays. However, the incorporation of automated systems into laboratory workflows is often hindered by the high cost and complexity associated with building robotic liquid handlers. Here, we report a 3D-printed liquid handler based on a fluidic manifold, thereby obviating the need for complex robotic mechanisms. The fluidic manifold, termed a dispensing and aspirating (DA) device, comprises parallelized multi-pipette structures connected by distribution and aspiration channels, enabling the precise supply and removal of reagents, respectively. Leveraging the versatility of 3D printing, the DA device can be custom-designed and printed to fit specific applications. As a proof-of-principle, we engineered a 3D-printed liquid handler dedicated for 3D digital rolling circle amplification (4DRCA), an advanced biochemical assay involving multiple sample preparation steps such as antibody incubation, cell fixation, nucleic acid amplification, probe hybridization, and extensive washing. We demonstrate the efficacy of the 3D-printed liquid handler to automate the preparation of clinical samples for the simultaneous, in situ analysis of oncogenic protein and transcript markers in B-cell acute lymphoblastic leukemia cells using 4DRCA. This approach provides an effective and accessible solution for liquid handling automation, offering high throughput and reproducibility in biochemical assays.

An Automated Versatile Diagnostic Workflow for Infectious Disease Detection in Low-Resource Settings

Laboratory automation effectively increases the throughput in sample analysis, reduces human errors in sample processing, as well as simplifies and accelerates the overall logistics. Automating diagnostic testing workflows in peripheral laboratories and also in near-patient settings -like hospitals, clinics and epidemic control checkpoints- is advantageous for the simultaneous processing of multiple samples to provide rapid results to patients, minimize the possibility of contamination or error during sample handling or transport, and increase efficiency. However, most automation platforms are expensive and are not easily adaptable to new protocols. Here, we address the need for a versatile, easy-to-use, rapid and reliable diagnostic testing workflow by combining open-source modular automation (Opentrons) and automation-compatible molecular biology protocols, easily adaptable to a workflow for infectious diseases diagnosis by detection on paper-based diagnostics. We demonstrated the feasibility of automation of the method with a low-cost Neisseria meningitidis diagnostic test that utilizes magnetic beads for pathogen DNA isolation, isothermal amplification, and detection on a paper-based microarray. In summary, we integrated open-source modular automation with adaptable molecular biology protocols, which was also faster and cheaper to perform in an automated than in a manual way. This enables a versatile diagnostic workflow for infectious diseases and we demonstrated this through a low-cost N. meningitidis test on paper-based microarrays.

The Duckbot: A system for automated imaging and manipulation of duckweed

Laboratory automation can boost precision and reproducibility of science workflows. However, current laboratory automation systems are difficult to modify for custom applications. Automating new experiment workflows therefore requires development of one-off research platforms, a process which requires significant time, resources, and experience. In this work, we investigate systems to lower the threshold to automation for plant biologists. Our approach establishes a direct connection with a generic motion platform to support experiment development and execution from a computational notebook environment. Specifically, we investigate the use of the open-source tool-changing motion platform Jubilee controlled using Jupyter notebooks. We present the Duckbot, a machine customized for automating laboratory research workflows with duckweed, a common multicellular plant. The Duckbot comprises (1) a set of end-effectors relevant for plant biology, (2) software modules which provide flexible control of these tools, and (3) computational notebooks which make use of these tools to automate duckweed experiments. We demonstrate the Duckbot's functionality by automating a particular laboratory research workflow, namely, duckweed growth assays. The Duckbot supports setting up sample plates with duckweed and growth media, gathering image data, and conducting relevant data analysis. We discuss the opportunities and limitations for developing custom laboratory automation with this platform and provide instructions on usage and customization.

Open hardware: From DIY trend to global transformation in access to laboratory equipment

Open hardware solutions are increasingly being chosen by researchers as a strategy to improve access to technology for cutting-edge biology research. The use of DIY technology is already widespread, particularly in countries with limited access to science funding, and is catalyzing the development of open-source technologies. Beyond financial accessibility, open hardware can be transformational for the access of laboratories to equipment by reducing dependence on import logistics and enabling direct knowledge transfer. Central drivers to the adoption of appropriate open-source technologies in biology laboratories around the world are open sharing, digital fabrication, local production, the use of standard parts, and detailed documentation. This Essay examines the global spread of open hardware and discusses which kinds of open-source technologies are the most beneficial in scientific environments with economic and infrastructural constraints.

Automation of yeast spot assays using an affordable liquid handling robot

The spot assay of the budding yeast Saccharomyces cerevisiae is an experimental method that is used to evaluate the effect of genotypes, medium conditions, and environmental stresses on cell growth and survival. Automation of the spot assay experiments from preparing a dilution series to spotting to observing spots continuously has been implemented based on large laboratory automation devices and robots, especially for high-throughput functional screening assays. However, there has yet to be an affordable solution for the automated spot assays suited to researchers in average laboratories and with high customizability for end-users. To make reproducible spot assay experiments widely available, we have automated the plate-based yeast spot assay of budding yeast using Opentrons OT-2 (OT-2), an affordable liquid-handling robot, and a flatbed scanner. We prepared a 3D-printed mount for the Petri dish to allow for precise placement of the Petri dish inside the OT-2. To account for the uneven height of the agar plates, which were made by human hands, we devised a method to adjust the z-position of the pipette tips based on the weight of each agar plate. During the incubation of the agar plates, a flatbed scanner was used to automatically take images of the agar plates over time, allowing researchers to quantify and compare the cell density within the spots at optimal time points a posteriori. Furthermore, the accuracy of the newly developed automated spot assay was verified by performing spot assays with human experimenters and the OT-2 and quantifying the yeast-grown area of the spots. This study will contribute to the introduction of automated spot assays and the automated acquisition of growth processes in conventional laboratories that are not adapted for high-throughput laboratory automation.

Mathematical and computational models in spheroid-based biofabrication

Ubiquitous in embryonic development, tissue fusion is of interest to tissue engineers who use tissue spheroids or organoids as building blocks of three-dimensional (3D) multicellular constructs. This review presents mathematical models and computer simulations of the fusion of tissue spheroids. The motivation of this study stems from the need to predict the post-printing evolution of 3D bioprinted constructs. First, we provide a brief overview of differential adhesion, the main morphogenetic mechanism involved in post-printing structure formation. It will be shown that clusters of cohesive cells behave as an incompressible viscous fluid on the time scale of hours. The discussion turns then to mathematical models based on the continuum hydrodynamics of highly viscous liquids and on statistical mechanics. Next, we analyze the validity and practical use of computational models of multicellular self-assembly in live constructs created by tissue spheroid bioprinting. Finally, we discuss the perspectives of the field as machine learning starts to reshape experimental design, and modular robotic workstations tend to alleviate the burden of repetitive tasks in biofabrication. STATEMENT OF SIGNIFICANCE: Bioprinted constructs are living systems, which evolve via morphogenetic mechanisms known from developmental biology. This review presents mathematical and computational tools devised for modeling post-printing structure formation. They help achieving a desirable outcome without expensive optimization experiments. While previous reviews mainly focused on assumptions, technical details, strengths, and limitations of computational models of multicellular self-assembly, this article discusses their validity and practical use in biofabrication. It also presents an overview of mathematical models that proved to be useful in the evaluation of experimental data on tissue spheroid fusion, and in the calibration of computational models. Finally, the perspectives of the field are discussed in the advent of robotic biofabrication platforms and bioprinting process optimization by machine learning.

Open Hardware in Science: The Benefits of Open Electronics

Openly shared low-cost electronic hardware applications, known as open electronics, have sparked a new open-source movement, with much untapped potential to advance scientific research. Initially designed to appeal to electronic hobbyists, open electronics have formed a global “maker” community and are increasingly used in science and industry. In this perspective article, we review the current costs and benefits of open electronics for use in scientific research ranging from the experimental to the theoretical sciences. We discuss how user-made electronic applications can help (I) individual researchers, by increasing the customization, efficiency, and scalability of experiments, while improving data quantity and quality; (II) scientific institutions, by improving access to customizable high-end technologies, sustainability, visibility, and interdisciplinary collaboration potential; and (III) the scientific community, by improving transparency and reproducibility, helping decouple research capacity from funding, increasing innovation, and improving collaboration potential among researchers and the public. We further discuss how current barriers like poor awareness, knowledge access, and time investments can be resolved by increased documentation and collaboration, and provide guidelines for academics to enter this emerging field. We highlight that open electronics are a promising and powerful tool to help scientific research to become more innovative and reproducible and offer a key practical solution to improve democratic access to science.

An Open-Source Modular Framework for Automated Pipetting and Imaging Applications

The number of samples in biological experiments is continuously increasing, but complex protocols and human error in many cases lead to suboptimal data quality and hence difficulties in reproducing scientific findings. Laboratory automation can alleviate many of these problems by precisely reproducing machine-readable protocols. These instruments generally require high up-front investments, and due to the lack of open application programming interfaces (APIs), they are notoriously difficult for scientists to customize and control outside of the vendor-supplied software. Here, automated, high-throughput experiments are demonstrated for interdisciplinary research in life science that can be replicated on a modest budget, using open tools to ensure reproducibility by combining the tools OpenFlexure, Opentrons, ImJoy, and UC2. This automated sample preparation and imaging pipeline can easily be replicated and established in many laboratories as well as in educational contexts through easy-to-understand algorithms and easy-to-build microscopes. Additionally, the creation of feedback loops, with later pipetting or imaging steps depending on the analysis of previously acquired images, enables the realization of fully autonomous "smart" microscopy experiments. All documents and source files are publicly available to prove the concept of smart lab automation using inexpensive, open tools. It is believed this democratizes access to the power and repeatability of automated experiments.

Mostly 3D printed chemical synthesis robot

Thanks to the current technology derived from the open-source world of 3D printers, it is conceivable to automate some laboratory activities remotely. In fact, simple operations, such as mixing liquids or solutions, stirring, heating and sampling to control the reaction course can be easily implemented. The idea of ​​automating the chemical laboratory would have immediate advantages, for example in terms of safety. The operators will be able to remotely control the machines and in case of handling dangerous material or accidents, there would only be damage to the hardware components. Many of the process parameters can also be read with low-cost probes and devices that can be easily interfaced with microprocessors. We include for example, but not limited to, temperature, pH, redox potential, electrochemical measurements in general or the use of probes for specific analytes. In this work we wish to present our liquid sampling station able to control up to 6 reagents and a temperature controlled chemical reactor. The workstation can be used graphically with an intuitive interface written in Python. The control program is structured to have modularity and contains a built-in programming language to control the interfaces.

Open source anaerobic and temperature-controlled in vitro model enabling real-time release studies with live bacteria

In vitro release and dissolution models are widely used in the development phases of oral drug delivery systems to measure how an active pharmaceutical ingredient (API) is released from a dosage form. However, additional requirements for these models arise when evaluating probiotic dosage forms since they are often sensitive to temperature and oxygen levels. As a solution to this, we propose a custom-designed anaerobic in vitro release setup, made mainly by 3D printing and laser cutting, to function together with state-of-the-art pharmaceutical dissolution equipment - in this case, a microDISS Profiler™. The in vitro release model makes it possible to study the release rate of oxygen-sensitive probiotics in simulated intestinal conditions, while ensuring their survival due to the anaerobic conditions. This has not been possible so far since the available in vitro dissolution models have not been compatible with anaerobic conditions. With two different case studies, the developed model combined with a microDISS Profiler™ has proven capable of measuring the release of a probiotic and a small-molecule API from microdevices for oral drug delivery. Further, the model facilitated the survival of anaerobic bacteria present in the release medium.

Automated melt electrowritting platform with real-time process monitoring

Melt electrowriting (MEW) is an additive manufacturing (AM) technology with the ability to fabricate complex designs with high-resolution. The utility of MEW is studied in many fields including tissue engineering and soft robotics. However, current MEW hardware offers only basic functionality and is often designed and built in-house. This affects results replication across different MEW devices and slows down the technological advancement. To address these issues, we present an automated MEW platform with real-time process parameter monitoring and control. We validate the developed platform by demonstrating the ability to accurately print polymer structures and successfully measure and adjust parameters during the printing process. The platform enables the collection of large volumes of data that can be subsequently used for further analysis of the system. Ultimately, the concept will help MEW to become more accessible for both research laboratories and industry and allow advancing the technology by leveraging the process monitoring, control and data collection.

Miau, a microbalance autosampler

Powder weighing is an essential but tedious activity in many branches of science. Here I describe a MIcrobalance AUtosampler (miau) that transfers solids in the sub-mg range to a microbalance. Miau is a pick-and-place machine which moves a gripper with dual function: 1) move tin capsules; 2) deliver powder from a container to tin capsules. In our laboratory we routinely use miau to prepare working standards for quality control of elemental and isotopic analyses. In a test, miau produced standards between 0.3 and 1.1 mg, which is a useful range in our laboratory. Failure to produce a weighed standard happened in 5% of the cases. A comparison with manual measurements demonstrated that obtained amounts for automated samples were as accurate and precise as manually prepared ones. Setup for daily use is simple, and the microbalance can be easily used alternately with or without miau. Miau is a low-cost device that can work with microbalances from many manufacturers, and can be readily adopted by many laboratories.

Open-hardware wireless controller and 3D-printed pumps for efficient liquid manipulation

Many routines in biological experiments require the precise handling of liquid volumes in the range of microliters up to liters. In this paper, we describe a new wireless controller that is adapted to liquid manipulation tasks, in particular when combined with the proposed 3D-printed pumps. It can be built from widely available electronic components and managed with open-source software. The use of peristaltic pumps enables to move volumes from milliliters to liters with a relative error below 1% or a syringe pump capable of injecting volumes in the range of milliliters with microliter accuracy. The system is remotely controllable over WiFi and easily automated using the MQTT communication protocol. The programming of the microcontroller is performed on the Arduino IDE. The WiFi settings and the calibration value can be easily modified, stored and exported in the form of a JSON file to create a user friendly, plug and play and easily scalable device. Additional sensors or actuators can be added, allowing the system to adapt to various usages. Finally, in addition to its low manufacturing cost and its capability to fit a large variety of tasks involving liquid handling, our system has been specifically designed for research environments where adaptability and repeatability of experiments is essential.

Automated 3D Microphysiometry Facilitates High-Content and Highly Reproducible Oxygen Measurements within 3D Cell Culture Models

Microphysiometry is a powerful technique to study metabolic parameters and detect changes to external stimuli. However, applying this technique for automated label-free and real-time measurements within cell-laden three-dimensional (3D) cell culture constructs remains a challenge. Herein, we present an entirely automated microphysiometry setup that combines needle-type microsensors with motorized sample and sensor positioning systems inside a standard tissue-culture incubator. The setup records dissolved oxygen as a metabolic parameter along the z-direction within cell-laden 3D constructs in a minimally invasive manner. The microphysiometry setup was applied to characterize the spatial oxygen distribution within thick cell-laden 3D constructs, study the time-dependent changes on the oxygen tension within 3D breast cancer models following a chemotherapeutic treatment, and identify kinetics and recovery effects after drug exposure over 5 weeks. Our data suggest that the microphysiometry setup enables highly reproducible measurements without human intervention, due to the high degree of automation and positional accuracy. The results demonstrate the applicability of the setup to provide valuable long-term insights into oxygenation within 3D models using minimally invasive, label-free, and entirely automated analysis methods.