The €100 lab: A 3D-printable open-source platform for fluorescence microscopy, optogenetics, and accurate temperature control during behaviour of zebrafish, Drosophila, and Caenorhabditis elegans

Open-source and low-cost miniature microscope for on-site fluorescence detection

The development of a compact and affordable fluorescence microscope can be a formidable challenge for growing needs in on-site testing and detection of fluorescent labeled biological systems, especially for those who specialize in biology rather than in engineering. In response to such a situation, we present an open-source miniature fluorescence microscope using Raspberry Pi. Our fluorescence microscope, with dimensions of 19.2 × 13.6 × 8.2 cm3 (including the display, computer, light-blocking case, and other operational requirements), not only offers cost-effectiveness (costing less than $500) but is also highly customizable to meet specific application needs. The 12.3-megapixel Raspberry Pi HQ Camera captures high-resolution imagery, while the equipped wide-angle lens provides a field of view measuring 21 × 15 mm2. The integrated wireless LAN in the Raspberry Pi, along with software-controllable high-powered fluorescence LEDs, holds potential for a wide range of applications. This open-source fluorescence microscope offers biohybrid sensor developers a versatile tool to streamline unfamiliar mechanical design tasks and open new opportunities for on-site fluorescence detections.

Orthogonal-view microscope for the biomechanics investigations of aquatic organisms

Microscopes are essential for the biomechanical and hydrodynamical investigation of small aquatic organisms. We report a prototype of a do-it-yourself microscope that enables the visualization of organisms from two orthogonal imaging planes - top and side views. Compared to conventional imaging systems, this approach provides a comprehensive visualization strategy of organisms, which could have complex shapes and morphologies. The microscope was constructed by combining custom 3D-printed parts and off-the-shelf components. The system is designed for modularity and reconfigurability. Open-source design files and build instructions are provided in this report. Additionally, proof-of-use experiments (particularly with Hydra) and other organisms that combine the imaging with an analysis pipeline were demonstrated to highlight the system's utility. Beyond the applications demonstrated, the system can be used or modified for various imaging applications.

Long-sperm precedence and other cryptic female choices in Drosophila melanogaster

Females that mate multiply make postmating choices about which sperm fertilize their eggs (cryptic female choice); however, the male characteristics they use to make such choices remain unclear. In this study, we sought to understand female sperm use patterns by evaluating whether Drosophila melanogaster females adjust sperm use (second male paternity) in response to four main factors: male genotype, male courtship effort, male pheromone alteration, and male postmating reproductive morphology. Our experiment was replicated across four different D. melanogaster lines, in a full factorial design, including a pheromone manipulation in which second males were perfumed to resemble heterospecific (D. yakuba) males. We found that females prefer longer sperm-regardless of mating order-in almost all contexts; this observed pattern of 'long-sperm precedence' is consistent with female postcopulatory choice of high-fitness male traits. Nonetheless, we also found that this general preference can be plastically altered by females in response to effects including perfuming treatment; this differential female sperm use is between otherwise identical males, and therefore solely female-mediated. Furthermore, our finding that females exercise choice using diverse criteria suggests a possible mechanism for the maintenance of variation in sexually selected male traits.

An open-source, high-resolution, automated fluorescence microscope

Fluorescence microscopy is a fundamental tool in the life sciences, but the availability of sophisticated equipment required to yield high-quality, quantitative data is a major bottleneck in data production in many laboratories worldwide. This problem has long been recognized and the abundancy of low-cost electronics and the simplification of fabrication through 3D-printing have led to the emergence of open-source scientific hardware as a research field. Cost effective fluorescence microscopes can be assembled from cheaply mass-produced components, but lag behind commercial solutions in image quality. On the other hand, blueprints of sophisticated microscopes such as light-sheet or super-resolution systems, custom-assembled from high quality parts, are available, but require a high level of expertise from the user. Here, we combine the UC2 microscopy toolbox with high-quality components and integrated electronics and software to assemble an automated high-resolution fluorescence microscope. Using this microscope, we demonstrate high resolution fluorescence imaging for fixed and live samples. When operated inside an incubator, long-term live-cell imaging over several days was possible. Our microscope reaches single molecule sensitivity, and we performed single particle tracking and SMLM super-resolution microscopy experiments in cells. Our setup costs a fraction of its commercially available counterparts but still provides a maximum of capabilities and image quality. We thus provide a proof of concept that high quality scientific data can be generated by lay users with a low-budget system and open-source software. Our system can be used for routine imaging in laboratories that do not have the means to acquire commercial systems and through its affordability can serve as teaching material to students.

pi_tailtrack: A compact, inexpensive and open-source behaviour-tracking system for head-restrained zebrafish

Quantifying animal behaviour during microscopy is crucial to associate optically recorded neural activity with behavioural outputs and states. Here, I describe an imaging and tracking system for head-restrained larval zebrafish compatible with functional microscopy. This system is based on the Raspberry Pi computer, Pi NoIR camera and open-source software for the real-time tail segmentation and skeletonization of the zebrafish tail at over 100 Hz. This allows for precise and long-term analyses of swimming behaviour, which can be related to functional signals recorded in individual neurons. This system offers a simple but performant solution for quantifying the behaviour of head-restrained larval zebrafish, which can be built for 340€.

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.

Orthogonal-view Microscope for the Biomechanics Investigations of Aquatic Organisms

Microscopes are essential for the biomechanical and hydrodynamical investigation of small aquatic organisms. We report a do-it-yourself microscope (GLUBscope) that enables the visualization of organisms from two orthogonal imaging planes - top and side views. Compared to conventional imaging systems, this approach provides a comprehensive visualization strategy of organisms, which could have complex shapes and morphologies. The microscope was constructed by combining custom 3D-printed parts and off-the-shelf components. The system is designed for modularity and reconfigurability. Open-source design files and build instructions are provided in this report. Additionally, proof-of-use experiments (particularly with Hydra) and other organisms that combine the GLUBscope with an analysis pipeline were demonstrated to highlight the system's utility. Beyond the applications demonstrated, the system can be used or modified for various imaging applications.

Dark-field light scattering microscope with focus stabilization

We present detailed design and operation instructions for a single-objective inverted microscope. Our design is suitable for two dark-field modes of operation: 1- total internal reflection scattering, and 2- cross-polarization backscattering. The user can switch between the two modes by exchanging one mode-steering element, which is also adapted to the Thorlabs cage system. To establish a stable background speckle for differential microscopy the imaging plane is stabilized with active feedback. We validate the stabilization efficacy by performing long-term scattering measurement on single nanoparticles. This setup can be extended for simultaneous scattering, fluorescence, and confocal imaging modes.

MicroFPGA: An affordable FPGA platform for microscope control

Modern microscopy relies increasingly on microscope automation to improve throughput, ensure reproducibility or observe rare events. Automation requires computer control of the important elements of the microscope. Furthermore, optical elements that are usually fixed or manually movable can be placed on electronically-controllable elements. In most cases, a central electronics board is necessary to generate the control signals they require and to communicate with the computer. For such tasks, Arduino microcontrollers are widely used due to their low cost and programming entry barrier. However, they are limiting in their performance for applications that require high-speed or multiple parallel processes. Field programmable gate arrays (FPGA) are the perfect technology for high-speed microscope control, as they are capable of processing signals in parallel and with high temporal precision. While plummeting prices made the technology available to consumers, a major hurdle remaining is the complex languages used to configure them. In this work, we used an affordable FPGA, delivered with an open-source and friendly-to-use programming language, to create a versatile microscope control platform called MicroFPGA. It is capable of synchronously triggering cameras and multiple lasers following complex patterns, as well as generating various signals used to control microscope elements such as filter wheels, servomotor stages, flip-mirrors, laser power or acousto-optic modulators. MicroFPGA is open-source and we provide online Micro-Manager, Java, Python and LabVIEW libraries, together with blueprints and tutorials.

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.

A novel post-developmental role of the Hox genes underlies normal adult behavior

The molecular mechanisms underlying the stability of mature neurons and neural circuits are poorly understood. Here we explore this problem and discover that the Hox genes are a component of the genetic program that maintains normal neural function in adult Drosophila. We show that post-developmental downregulation of the Hox gene Ultrabithorax (Ubx) in adult neurons leads to substantial anomalies in flight. Mapping the cellular basis of these effects reveals that Ubx is required within a subset of dopaminergic neurons, and cell circuitry analyses in combination with optogenetics allow us to link these dopaminergic neurons to flight control. Functional imaging experiments show that Ubx is necessary for normal dopaminergic activity, and neuron-specific RNA-sequencing defines two previously uncharacterized ion channel-encoding genes as potential mediators of Ubx behavioral roles. Our study thus reveals a novel role of the Hox system in controlling adult behavior and neural function. Based on the broad evolutionary conservation of the Hox system across distantly related animal phyla, we predict that the Hox genes might play neurophysiological roles in adult forms of other species, including humans.

Rapid Bacterial Motility Monitoring Using Inexpensive 3D-Printed OpenFlexure Microscopy Allows Microfluidic Antibiotic Susceptibility Testing

Antibiotic susceptibility testing is vital to tackle the emergence and spread of antimicrobial resistance. Inexpensive digital CMOS cameras can be converted into portable digital microscopes using 3D printed x-y-z stages. Microscopic examination of bacterial motility can rapidly detect the response of microbes to antibiotics to determine susceptibility. Here, we present a new simple microdevice-miniature microscope cell measurement system for multiplexed antibiotic susceptibility testing. The microdevice is made using melt-extruded plastic film strips containing ten parallel 0.2 mm diameter microcapillaries. Two different antibiotics, ceftazidime and gentamicin, were prepared in Mueller-Hinton agar (0.4%) to produce an antibiotic-loaded microdevice for simple sample addition. This combination was selected to closely match current standard methods for both antibiotic susceptibility testing and motility testing. Use of low agar concentration permits observation of motile bacteria responding to antibiotic exposure as they enter capillaries. This device fits onto the OpenFlexure 3D-printed digital microscope using a Raspberry Pi computer and v2 camera, avoiding need for expensive laboratory microscopes. This inexpensive and portable digital microscope platform had sufficient magnification to detect motile bacteria, yet wide enough field of view to monitor bacteria behavior as they entered antibiotic-loaded microcapillaries. The image quality was sufficient to detect how bacterial motility was inhibited by different concentrations of antibiotic. We conclude that a 3D-printed Raspberry Pi-based microscope combined with disposable microfluidic test strips permit rapid, easy-to-use bacterial motility detection, with potential for aiding detection of antibiotic resistance.

Low-cost modular systems for agarose gel documentation

While conducting recombinant DNA technology procedures, such as DNA purification, agarose gel electrophoresis is often used for identification, characterization and quantification of DNA. The collection of data for experiments involving such techniques frequently involves capturing images using systems that are expensive and/or proprietary, such that they are not user-serviceable when they malfunction or become antiquated. In response to these limitations, work was done to replace the authors' existing aging Mac OS-based modular system with open-source software and generic hardware. Several versions of a modular imaging system that can be adjusted to fit nearly all use cases are described. The systems developed can accommodate diverse uses from research laboratories to educational environments where commercial systems could be unaffordable.

PiSpy: An affordable, accessible, and flexible imaging platform for the automated observation of organismal biology and behavior

A great deal of understanding can be gleaned from direct observation of organismal growth, development, and behavior. However, direct observation can be time consuming and influence the organism through unintentional stimuli. Additionally, video capturing equipment can often be prohibitively expensive, difficult to modify to one's specific needs, and may come with unnecessary features. Here, we describe PiSpy, a low-cost, automated video acquisition platform that uses a Raspberry Pi computer and camera to record video or images at specified time intervals or when externally triggered. All settings and controls, such as programmable light cycling, are accessible to users with no programming experience through an easy-to-use graphical user interface. Importantly, the entire PiSpy system can be assembled for less than $100 using laser-cut and 3D-printed components. We demonstrate the broad applications and flexibility of PiSpy across a range of model and non-model organisms. Designs, instructions, and code can be accessed through an online repository, where a global community of PiSpy users can also contribute their own unique customizations and help grow the community of open-source research solutions.

PiRamid: A compact Raspberry Pi imaging box to automate small-scale time-lapse digital analysis, suitable for laboratory and field use

Digital imaging permits the quantitation of many experiments, such as microbiological growth assays, but laboratory digital imaging systems can be expensive and too specialised. The Raspberry Pi camera platform makes automated, controlled imaging affordable with accessible customisation. When combined with open source software and open-source 3D printed hardware, the control over image quality and capture of this platform permits the rapid development of novel instrumentation. Here we present "PiRamid", a compact, portable, and inexpensive enclosure for autonomous imaging both in the laboratory and in the field. The modular three-piece 3D printed design makes it easy to incorporate different camera systems or lighting configurations (e.g., single wavelength LED for fluorescence). The enclosed design allows complete control of illumination unlike a conventional digital camera or smartphone, on a tripod or handheld, under ambient lighting. The stackable design permits rapid sample addition or camera focus adjustment, with a corresponding change in magnification and resolution. The entire unit is small enough to fit within a microbiological incubator, and cheap enough (∼£100) to scale out for larger parallel experiments. Simply, Python scripts fully automate illumination and image capture for small-scale experiments with an ∼110×85 mm area at 70-90 µm resolution. We demonstrate the versatility of PiRamid by capturing time-resolved, quantitative image data for a wide range of assays. Bacterial growth kinetics was captured for conventional microbiology (agar Petri dishes), 3D printed custom microbiology labware and microfluidic microbiology. To illustrate application beyond microbiology, we demonstrate time-lapse imaging of crystal growth and degradation of salad leaves. Minor modifications permit epi-illumination by addition of a LED ring to the camera module. We conclude that PiRamid permits inexpensive digital capture and quantitation of a wide range of experiments by time-lapse imaging to simplify both laboratory and field imaging.

Utilising low-cost, easy-to-use microscopy techniques for early peritonitis infection screening in peritoneal dialysis patients

Peritoneal dialysis (PD) patients are at high risk for peritonitis, an infection of the peritoneum that affects 13% of PD users annually. Relying on subjective peritonitis symptoms results in delayed treatment, leading to high hospitalisation costs, peritoneal scarring, and premature transition to haemodialysis. We have developed and tested a low-cost, easy-to-use technology that uses microscopy and image analysis to screen for peritonitis across the effluent drain tube. Compared to other technologies, our prototype is made from off-the-shelf, low-cost materials. It can be set up quickly and key stakeholders believe it can improve the overall PD experience. We demonstrate that our prototype classifies infection-indicating and healthy white blood cell levels in clinically collected patient effluent with 94% accuracy. Integration of our technology into PD setups as a screening tool for peritonitis would enable earlier physician notification, allowing for prompt diagnosis and treatment to prevent hospitalisations, reduce scarring, and increase PD longevity. Our findings demonstrate the versatility of microscopy and image analysis for infection screening and are a proof of principle for their future applications in health care.

A low-cost, open-source centrifuge adaptor for separating large volume clinical blood samples

Blood plasma separation is a prerequisite in numerous biomedical assays involving low abundance plasma-borne biomarkers and thus is the fundamental step before many bioanalytical steps. High-capacity refrigerated centrifuges, which have the advantage of handling large volumes of blood samples, are widely utilized, but they are bulky, non-transportable, and prohibitively expensive for low-resource settings, with prices starting at $1,500. On the other hand, there are low-cost commercial and open-source micro-centrifuges available, but they are incapable of handling typical clinical amounts of blood samples (2-10mL). There is currently no low-cost CE marked centrifuge that can process large volumes of clinical blood samples on the market. As a solution, we customised the rotor of a commercially available low-cost micro-centrifuge (~$125) using 3D printing to enable centrifugation of large clinical blood samples in resource poor-settings. Our custom adaptor ($15) can hold two 9 mL S-Monovette tubes and achieve the same separation performance (yield, cell count, hemolysis, albumin levels) as the control benchtop refrigerated centrifuge, and even outperformed the control in platelet separation by at least four times. This low-cost open-source centrifugation system capable of processing clinical blood tubes could be valuable to low-resource settings where centrifugation is required immediately after blood withdrawal for further testing.

Optical sectioning robotic microscopy for everyone: the structured illumination microscope with the OpenFlexure stages

We report on the 3D-printed structured illumination microscope (SIM) with optical sectioning capability. Optically sectioned images are obtained by projecting a single-spatial-frequency grid pattern onto the specimen and recording three images with the grid pattern at different spatial phases, and then post-processing with simple mathematics. For the precise actuation of the grid for the structured illumination and the positioning of the sample, stages of the open-sourced, 3D-printable OpenFlexure families, which are capable of highly precise positioning control of tens of nanometers based on the flexure mechanism of the flexible plastics, are utilized. Our system has optical sectioning strength of a few microns, which is equivalent to that achievable with the confocal microscopes. The operation of our system can be automated with the Raspberry Pi and can be remotely operated from a PC via a wireless local area network.

A Cost-Effective Nucleic Acid Detection System Using a Portable Microscopic Device

A fluorescence microscope is one of the most important tools for biomedical research and laboratory diagnosis. However, its high cost and bulky size hinder the application of laboratory microscopes in space-limited and low-resource applications. Here, in this work, we proposed a portable and cost-effective fluorescence microscope. Assembled from a set of 3D print components and a webcam, it consists of a three-degree-of-freedom sliding platform and a microscopic imaging system. The microscope is capable of bright-field and fluorescence imaging with micron-level resolution. The resolution and field of view of the microscope were evaluated. Compared with a laboratory-grade inverted fluorescence microscope, the portable microscope shows satisfactory performance, both in the bright-field and fluorescence mode. From the configurations of local resources, the microscope costs around USD 100 to assemble. To demonstrate the capability of the portable fluorescence microscope, we proposed a quantitative polymerase chain reaction experiment for meat product authenticating applications. The portable and low-cost microscope platform demonstrates the benefits in space-constrained environments and shows high potential in telemedicine, point-of-care testing, and more.

Automated Open-Hardware Multiwell Imaging Station for Microorganisms Observation

Bright field microscopes are particularly useful tools for biologists for cell and tissue observation, phenotyping, cell counting, and so on. Direct cell observation provides a wealth of information on cells’ nature and physiological condition. Microscopic analyses are, however, time-consuming and usually not easy to parallelize. We describe the fabrication of a stand-alone microscope able to automatically collect samples with 3D printed pumps, and capture images at up to 50× optical magnification with a digital camera at a good throughput (up to 24 different samples can be collected and scanned in less than 10 min). Furthermore, the proposed device can store and analyze pictures using computer vision algorithms running on a low power integrated single board computer. Our device can perform a large set of tasks, with minimal human intervention, that no single commercially available machine can perform. The proposed open-hardware device has a modular design and can be freely reproduced at a very competitive price with the use of widely documented and user-friendly components such as Arduino, Raspberry pi, and 3D printers.

An optogenetics device with smartphone video capture to introduce neurotechnology and systems neuroscience to high school students

Although neurotechnology careers are on the rise, and neuroscience curriculums have significantly grown at the undergraduate and graduate levels, increasing neuroscience and neurotechnology exposure in high school curricula has been an ongoing challenge. This is due, in part, to difficulties in converting cutting-edge neuroscience research into hands-on activities that are accessible for high school students and affordable for high school educators. Here, we describe and characterize a low-cost, easy-to-construct device to enable students to record rapid Drosophila melanogaster (fruit fly) behaviors during optogenetics experiments. The device is generated from inexpensive Arduino kits and utilizes a smartphone for video capture, making it easy to adopt in a standard biology laboratory. We validate this device is capable of replicating optogenetics experiments performed with more sophisticated setups at leading universities and institutes. We incorporate the device into a high school neuroengineering summer workshop. We find student participation in the workshop significantly enhances their understanding of key neuroscience and neurotechnology concepts, demonstrating how this device can be utilized in high school settings and undergraduate research laboratories seeking low-cost alternatives.

Schistoscope: An Automated Microscope with Artificial Intelligence for Detection of Schistosoma haematobium Eggs in Resource-Limited Settings

For many parasitic diseases, the microscopic examination of clinical samples such as urine and stool still serves as the diagnostic reference standard, primarily because microscopes are accessible and cost-effective. However, conventional microscopy is laborious, requires highly skilled personnel, and is highly subjective. Requirements for skilled operators, coupled with the cost and maintenance needs of the microscopes, which is hardly done in endemic countries, presents grossly limited access to the diagnosis of parasitic diseases in resource-limited settings. The urgent requirement for the management of tropical diseases such as schistosomiasis, which is now focused on elimination, has underscored the critical need for the creation of access to easy-to-use diagnosis for case detection, community mapping, and surveillance. In this paper, we present a low-cost automated digital microscope—the Schistoscope—which is capable of automatic focusing and scanning regions of interest in prepared microscope slides, and automatic detection of Schistosoma haematobium eggs in captured images. The device was developed using widely accessible distributed manufacturing methods and off-the-shelf components to enable local manufacturability and ease of maintenance. For proof of principle, we created a Schistosoma haematobium egg dataset of over 5000 images captured from spiked and clinical urine samples from field settings and demonstrated the automatic detection of Schistosoma haematobium eggs using a trained deep neural network model. The experiments and results presented in this paper collectively illustrate the robustness, stability, and optical performance of the device, making it suitable for use in the monitoring and evaluation of schistosomiasis control programs in endemic settings.

The Field Guide to 3D Printing in Optical Microscopy for Life Sciences

The maker movement has reached the optics labs, empowering researchers to create and modify microscope designs and imaging accessories. 3D printing has a disruptive impact on the field, improving accessibility to fabrication technologies in additive manufacturing. This approach is particularly useful for rapid, low-cost prototyping, allowing unprecedented levels of productivity and accessibility. From inexpensive microscopes for education such as the FlyPi to the highly complex robotic microscope OpenFlexure, 3D printing is paving the way for the democratization of technology, promoting collaborative environments between researchers, as 3D designs are easily shared. This holds the unique possibility of extending the open-access concept from knowledge to technology, allowing researchers everywhere to use and extend model structures. Here, it is presented a review of additive manufacturing applications in optical microscopy for life sciences, guiding the user through this new and exciting technology and providing a starting point to anyone willing to employ this versatile and powerful new tool.

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.

Deep learning for robust and flexible tracking in behavioral studies for C. elegans

Robust and accurate behavioral tracking is essential for ethological studies. Common methods for tracking and extracting behavior rely on user adjusted heuristics that can significantly vary across different individuals, environments, and experimental conditions. As a result, they are difficult to implement in large-scale behavioral studies with complex, heterogenous environmental conditions. Recently developed deep-learning methods for object recognition such as Faster R-CNN have advantages in their speed, accuracy, and robustness. Here, we show that Faster R-CNN can be employed for identification and detection of Caenorhabditis elegans in a variety of life stages in complex environments. We applied the algorithm to track animal speeds during development, fecundity rates and spatial distribution in reproductive adults, and behavioral decline in aging populations. By doing so, we demonstrate the flexibility, speed, and scalability of Faster R-CNN across a variety of experimental conditions, illustrating its generalized use for future large-scale behavioral studies.

Open-source 3D-printed terahertz pulse time-domain holographic detection module

We present a holographic detection module to measure the spatially resolved distribution of pulsed terahertz field in a single scan by a motorized translation stage, responsible for the time delay. All mounts of the optical elements of the module are easily reproduced by 3D printing and attached to the optical cage system. The latter greatly simplifies the measurement procedure, allowing the experimenter to move and adjust the detection system as a single device. The developed mounts are made universal and can be used in other setups. We have made 3D models available as open-source hardware. The module is based on an electro-optical detection scheme with wide-aperture ZnTe crystal, crossed polarizers, and a matrix photodetector. The validation of its operability was performed with two experiments to measure the spatial distribution of the unperturbed field from the generator and the vortex field formed by the spiral phase plate. Optical vortices with multiple topological charges of 2-4 were detected on spectral components in the range from 0.3 to 1.1 THz. In addition, we have detailed the alignment process of terahertz imaging systems.

Phenotyping of Drosophila melanogaster—A Nutritional Perspective

The model organism Drosophila melanogaster was increasingly applied in nutrition research in recent years. A range of methods are available for the phenotyping of D. melanogaster, which are outlined in the first part of this review. The methods include determinations of body weight, body composition, food intake, lifespan, locomotor activity, reproductive capacity and stress tolerance. In the second part, the practical application of the phenotyping of flies is demonstrated via a discussion of obese phenotypes in response to high-sugar diet (HSD) and high-fat diet (HFD) feeding. HSD feeding and HFD feeding are dietary interventions that lead to an increase in fat storage and affect carbohydrate-insulin homeostasis, lifespan, locomotor activity, reproductive capacity and stress tolerance. Furthermore, studies regarding the impacts of HSD and HFD on the transcriptome and metabolome of D. melanogaster are important for relating phenotypic changes to underlying molecular mechanisms. Overall, D. melanogaster was demonstrated to be a valuable model organism with which to examine the pathogeneses and underlying molecular mechanisms of common chronic metabolic diseases in a nutritional context.

Methods for rapid prototyping novel labware: using CAD and desktop 3D printing in the microbiology laboratory

Although the microbiology laboratory paradigm has increasingly changed from manual to automated procedures, and from functional to molecular methods, traditional culture methods remain vital. Using inexpensive desktop fused filament fabrication 3D printing, we designed, produced and tested rapid prototypes of customised labware for microbial culture namely frames to make dip slides, inoculation loops, multi-pin replicators, and multi-well culture plates for solid medium. These customised components were used to plate out samples onto solid media in various formats, and we illustrate how they can be suitable for many microbiological methods such as minimum inhibitory concentration tests, or for directly detecting pathogens from mastitis samples, illustrating the flexibility of rapid-prototyped culture consumable parts for streamlining microbiological methods. We describe the methodology needed for microbiologists to develop their own novel and unique tools, or to fabricate and customise existing consumables. A workflow is presented for designing and 3D printing labware and quickly producing easy-to-sterilise and re-useable plastic parts of great utility in the microbiology laboratory.

Picroscope: low-cost system for simultaneous longitudinal biological imaging

Simultaneous longitudinal imaging across multiple conditions and replicates has been crucial for scientific studies aiming to understand biological processes and disease. Yet, imaging systems capable of accomplishing these tasks are economically unattainable for most academic and teaching laboratories around the world. Here, we propose the Picroscope, which is the first low-cost system for simultaneous longitudinal biological imaging made primarily using off-the-shelf and 3D-printed materials. The Picroscope is compatible with standard 24-well cell culture plates and captures 3D z-stack image data. The Picroscope can be controlled remotely, allowing for automatic imaging with minimal intervention from the investigator. Here, we use this system in a range of applications. We gathered longitudinal whole organism image data for frogs, zebrafish, and planaria worms. We also gathered image data inside an incubator to observe 2D monolayers and 3D mammalian tissue culture models. Using this tool, we can measure the behavior of entire organisms or individual cells over long-time periods.

MicroHikari3D: an automated DIY digital microscopy platform with deep learning capabilities

A microscope is an essential tool in biosciences and production quality laboratories for unveiling the secrets of microworlds. This paper describes the development of MicroHikari3D, an affordable DIY optical microscopy platform with automated sample positioning, autofocus and several illumination modalities to provide a high-quality flexible microscopy tool for labs with a short budget. This proposed optical microscope design aims to achieve high customization capabilities to allow whole 2D slide imaging and observation of 3D live specimens. The MicroHikari3D motion control system is based on the entry level 3D printer kit Tronxy X1 controlled from a server running in a Raspberry Pi 4. The server provides services to a client mobile app for video/image acquisition, processing, and a high level classification task by applying deep learning models.

An Open-Source Framework for Automated High-Throughput Cell Biology Experiments

Modern data analysis methods, such as optimization algorithms or deep learning have been successfully applied to a number of biotechnological and medical questions. For these methods to be efficient, a large number of high-quality and reproducible experiments needs to be conducted, requiring a high degree of automation. Here, we present an open-source hardware and low-cost framework that allows for automatic high-throughput generation of large amounts of cell biology data. Our design consists of an epifluorescent microscope with automated XY stage for moving a multiwell plate containing cells and a perfusion manifold allowing programmed application of up to eight different solutions. Our system is very flexible and can be adapted easily for individual experimental needs. To demonstrate the utility of the system, we have used it to perform high-throughput Ca2+ imaging and large-scale fluorescent labeling experiments.

Quantitative particle agglutination assay for point-of-care testing using mobile holographic imaging and deep learning

Particle agglutination assays are widely adopted immunological tests that are based on antigen-antibody interactions. Antibody-coated microscopic particles are mixed with a test sample that potentially contains the target antigen, as a result of which the particles form clusters, with a size that is a function of the antigen concentration and the reaction time. Here, we present a quantitative particle agglutination assay that combines mobile lens-free microscopy and deep learning for rapidly measuring the concentration of a target analyte; as its proof-of-concept, we demonstrate high-sensitivity C-reactive protein (hs-CRP) testing using human serum samples. A dual-channel capillary lateral flow device is designed to host the agglutination reaction using 4 μL of serum sample with a material cost of 1.79 cents per test. A mobile lens-free microscope records time-lapsed inline holograms of the lateral flow device, monitoring the agglutination process over 3 min. These captured holograms are processed, and at each frame the number and area of the particle clusters are automatically extracted and fed into shallow neural networks to predict the CRP concentration. 189 measurements using 88 unique patient serum samples were utilized to train, validate and blindly test our platform, which matched the corresponding ground truth concentrations in the hs-CRP range (0-10 μg mL^-1) with an R² value of 0.912. This computational sensing platform was also able to successfully differentiate very high CRP concentrations (e.g., >10-500 μg mL^-1) from the hs-CRP range. This mobile, cost-effective and quantitative particle agglutination assay can be useful for various point-of-care sensing needs and global health related applications.

An Inexpensive, High-Precision, Modular Spherical Treadmill Setup Optimized for Drosophila Experiments

To pursue a more mechanistic understanding of the neural control of behavior, many neuroethologists study animal behavior in controlled laboratory environments. One popular approach is to measure the movements of restrained animals while presenting controlled sensory stimulation. This approach is especially powerful when applied to genetic model organisms, such as Drosophila melanogaster, where modern genetic tools enable unprecedented access to the nervous system for activity monitoring or targeted manipulation. While there is a long history of measuring the behavior of body- and head-fixed insects walking on an air-supported ball, the methods typically require complex setups with many custom components. Here we present a compact, simplified setup for these experiments that achieves high-performance at low cost. The simplified setup integrates existing hardware and software solutions with new component designs. We replaced expensive optomechanical and custom machined components with off-the-shelf and 3D-printed parts, and built the system around a low-cost camera that achieves 180 Hz imaging and an inexpensive tablet computer to present view-angle-corrected stimuli updated through a local network. We quantify the performance of the integrated system and characterize the visually guided behavior of flies in response to a range of visual stimuli. In this paper, we thoroughly document the improved system; the accompanying repository incorporates CAD files, parts lists, source code, and detailed instructions. We detail a complete ~$300 system, including a cold-anesthesia tethering stage, that is ideal for hands-on teaching laboratories. This represents a nearly 50-fold cost reduction as compared to a typical system used in research laboratories, yet is fully featured and yields excellent performance. We report the current state of this system, which started with a 1-day teaching lab for which we built seven parallel setups and continues toward a setup in our lab for larger-scale analysis of visual-motor behavior in flies. Because of the simplicity, compactness, and low cost of this system, we believe that high-performance measurements of tethered insect behavior should now be widely accessible and suitable for integration into many systems. This access enables broad opportunities for comparative work across labs, species, and behavioral paradigms.

Two decades of neuroscience publication trends in Africa

Neuroscience research in Africa remains sparse. Devising new policies to boost Africa's neuroscience landscape is imperative, but these must be based on accurate data on research outputs which is largely lacking. Such data must reflect the heterogeneity of research environments across the continent's 54 countries. Here, we analyse neuroscience publications affiliated with African institutions between 1996 and 2017. Of 12,326 PubMed indexed publications, 5,219 show clear evidence that the work was performed in Africa and led by African-based researchers - on average ~5 per country and year. From here, we extract information on journals and citations, funding, international coauthorships and techniques used. For reference, we also extract the same metrics from 220 randomly selected publications each from the UK, USA, Australia, Japan and Brazil. Our dataset provides insights into the current state of African neuroscience research in a global context.

The steroid-hormone ecdysone coordinates parallel pupariation neuromotor and morphogenetic subprograms via epidermis-to-neuron Dilp8-Lgr3 signal induction

Innate behaviors consist of a succession of genetically-hardwired motor and physiological subprograms that can be coupled to drastic morphogenetic changes. How these integrative responses are orchestrated is not completely understood. Here, we provide insight into these mechanisms by studying pupariation, a multi-step innate behavior of Drosophila larvae that is critical for survival during metamorphosis. We find that the steroid-hormone ecdysone triggers parallel pupariation neuromotor and morphogenetic subprograms, which include the induction of the relaxin-peptide hormone, Dilp8, in the epidermis. Dilp8 acts on six Lgr3-positive thoracic interneurons to couple both subprograms in time and to instruct neuromotor subprogram switching during behavior. Our work reveals that interorgan feedback gates progression between subunits of an innate behavior and points to an ancestral neuromodulatory function of relaxin signaling.

Chronic Optogenetic Stimulation in Freely Moving Rodents

In vivo optogenetic strategies have been fundamental for the investigation of how neural circuits relate to behavior. While short-term experimental procedures are typically used in such studies, chronic stimulation during behavioral sessions has been largely unexplored. Here we describe a protocol for long-term optogenetic modulation of neuronal populations in freely moving animals.

Building Your Own Neuroscience Equipment: A Precision Micromanipulator and an Epi-fluorescence Microscope for Calcium Imaging

A faculty member's ability to develop meaningful research-oriented laboratories in neurobiology is often hampered by the rapid pace of new technologies and the increasing cost of equipment. To help undergraduate neuroscience faculty meet these challenges, we introduce two important neuroscience research tools we designed and built. The first is a precision micromanipulator for neurophysiology applications costing less than $40 USD. We compare data generated using the DIY manipulator with commercial micromanipulators costing over $1000. The second tool is our newly designed 3D printed epi-fluorescence microscope. Commercial fluorescence imaging devices often cost over $20,000, but our 3D printed version is constructed for less than $1200. This epi-fluorescence microscope uses interchangeable LED light sources and filter sets to image static fluorescence in prepared slides and calcium imaging of neuronal activity in living Drosophila brains. This later technique uses transgenic flies with a genetically encoded calcium indicator, GCaMP, linked to green fluorescent protein (GFP). During an action potential, calcium ions (Ca2+) enter neurons and are observed as an increase in fluorescence intensity from a series of video images. These neuronal firing patterns can be assessed qualitatively and quantitatively to understand neural circuits leading to specific behaviors. We plan to develop curricula around the use of the epi-fluorescence microscope for calcium imaging in the next year, and to provide detailed parts sources and construction guides for the student and faculty DIY experience.

Inexpensive Methods for Live Imaging of Central Pattern Generator Activity in the Drosophila Larval Locomotor System

Central pattern generators (CPGs) are neural networks that produce rhythmic motor activity in the absence of sensory input. CPGs produce 'fictive' behaviours in vitro which parallel activity seen in intact animals. CPG networks have been identified in a wide variety of model organisms and have been shown to be critical for generating rhythmic behaviours such as swimming, walking, chewing and breathing. Work with CPG preparations has led to fundamental advances in neuroscience; however, most CPG preparations involve intensive dissections and require sophisticated electrophysiology equipment, making export to teaching laboratories problematic. Here we present an integrated approach for bringing the study of locomotor CPGs in Drosophila larvae into teaching laboratories. First, we present freely available genetic constructs that enable educators to express genetically encoded calcium indicators in cells of interest in the larval central nervous system. Next, we describe how to isolate the larval central nervous system and prepare it for live imaging. We then show how to modify standard compound microscopes to enable fluorescent imaging using 3D printed materials and inexpensive optical components. Finally, we show how to use the free image analysis programme ImageJ and freely available features in the signal analysis programme DataView to analyse rhythmic CPG activity in the larval CNS. Comparison of results to those obtained on research equipment shows that signal-to-noise levels are comparable and core features of larval CPG activity can be observed. Overall, this work shows the viability of exporting live imaging experiments to low cost environments and paves the way for new teaching laboratory exercises revolving around optical imaging of CPG activity.

A versatile and customizable low-cost 3D-printed open standard for microscopic imaging

Modern microscopes used for biological imaging often present themselves as black boxes whose precise operating principle remains unknown, and whose optical resolution and price seem to be in inverse proportion to each other. With UC2 (You. See. Too.) we present a low-cost, 3D-printed, open-source, modular microscopy toolbox and demonstrate its versatility by realizing a complete microscope development cycle from concept to experimental phase. The self-contained incubator-enclosed brightfield microscope monitors monocyte to macrophage cell differentiation for seven days at cellular resolution level (e.g. 2 μm). Furthermore, by including very few additional components, the geometry is transferred into a 400 Euro light sheet fluorescence microscope for volumetric observations of a transgenic Zebrafish expressing green fluorescent protein (GFP). With this, we aim to establish an open standard in optics to facilitate interfacing with various complementary platforms. By making the content and comprehensive documentation publicly available, the systems presented here lend themselves to easy and straightforward replications, modifications, and extensions.

Open standard microscopy is urgently needed to give low-cost solutions to researchers and to overcome the reproducibility crisis in science. Here the authors present a 3D-printed, open-source modular microscopy toolbox UC2 (You. See. Too.) for a few hundred Euros.

SiCTeC: An inexpensive, easily assembled Peltier device for rapid temperature shifting during single-cell imaging

Single-cell imaging, combined with recent advances in image analysis and microfluidic technologies, have enabled fundamental discoveries of cellular responses to chemical perturbations that are often obscured by traditional liquid-culture experiments. Temperature is an environmental variable well known to impact growth and to elicit specific stress responses at extreme values; it is often used as a genetic tool to interrogate essential genes. However, the dynamic effects of temperature shifts have remained mostly unstudied at the single-cell level, due largely to engineering challenges related to sample stability, heatsink considerations, and temperature measurement and feedback. Additionally, the few commercially available temperature-control platforms are costly. Here, we report an inexpensive (<$110) and modular Single-Cell Temperature Controller (SiCTeC) device for microbial imaging-based on straightforward modifications of the typical slide-sample-coverslip approach to microbial imaging-that controls temperature using a ring-shaped Peltier module and microcontroller feedback. Through stable and precise (±0.15°C) temperature control, SiCTeC achieves reproducible and fast (1-2 min) temperature transitions with programmable waveforms between room temperature and 45°C with an air objective. At the device's maximum temperature of 89°C, SiCTeC revealed that Escherichia coli cells progressively shrink and lose cellular contents. During oscillations between 30°C and 37°C, cells rapidly adapted their response to temperature upshifts. Furthermore, SiCTeC enabled the discovery of rapid morphological changes and enhanced sensitivity to substrate stiffness during upshifts to nonpermissive temperatures in temperature-sensitive mutants of cell-wall synthesis enzymes. Overall, the simplicity and affordability of SiCTeC empowers future studies of the temperature dependence of single-cell physiology.

Fovea-like Photoreceptor Specializations Underlie Single UV Cone Driven Prey-Capture Behavior in Zebrafish

In the eye, the function of same-type photoreceptors must be regionally adjusted to process a highly asymmetrical natural visual world. Here, we show that UV cones in the larval zebrafish area temporalis are specifically tuned for UV-bright prey capture in their upper frontal visual field, which may use the signal from a single cone at a time. For this, UV-photon detection probability is regionally boosted more than 10-fold. Next, in vivo two-photon imaging, transcriptomics, and computational modeling reveal that these cones use an elevated baseline of synaptic calcium to facilitate the encoding of bright objects, which in turn results from expressional tuning of phototransduction genes. Moreover, the light-driven synaptic calcium signal is regionally slowed by interactions with horizontal cells and later accentuated at the level of glutamate release driving retinal networks. These regional differences tally with variations between peripheral and foveal cones in primates and hint at a common mechanistic origin.

PiVR: An affordable and versatile closed-loop platform to study unrestrained sensorimotor behavior

Tools enabling closed-loop experiments are crucial to delineate causal relationships between the activity of genetically labeled neurons and specific behaviors. We developed the Raspberry Pi Virtual Reality (PiVR) system to conduct closed-loop optogenetic stimulation of neural functions in unrestrained animals. PiVR is an experimental platform that operates at high temporal resolution (70 Hz) with low latencies (<30 milliseconds), while being affordable ( Collapse

Key Words Collapse

MESH Headings

• Animals
• Behavior, Animal/physiology
• Chemotaxis
• Drosophila melanogaster/physiology
• Larva/physiology
• Light
• Locomotion
• Male
• Neurons/physiology
• Odorants
• Optogenetics
• Sensation/physiology
• Sensorimotor Cortex/physiology
• Software
• Taste/physiology
• Virtual Reality
• Zebrafish

Collapse

Grants

• R01 NS113048 NINDS NIH HHS
• R25 GM067110 NIGMS NIH HHS
• National Science Foundation
• National Institute of Health
• Gordon and Betty Moore Foundation

Collapse

Affiliation(s)

David Tadres Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, United States of America Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, United States of America Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland

Matthieu Louis Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, United States of America Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, United States of America Department of Physics, University of California, Santa Barbara, Santa Barbara, California, United States of America

Collapse

Twister3: a simple and fast microwire twister

Objective.

Twisted wire probes (TWPs, e.g. stereotrodes and tetrodes) provide a cheap and reliable method for obtaining high quality, multiple single-unit neural recordings in freely moving animals. Despite their ubiquity, TWPs are constructed using a tedious procedure consisting of manually folding, turning, and fusing microwire. This imposes a significant labor burden on research personnel who use TWPs in their experiments.

Approach.

To address this issue, we created Twister3, an open-source microwire twisting machine. This machine features a quick-draw wire feeder that eliminates manual wire folding, an auto-aligning motor attachment mechanism which results in consistently straight probes, and a high speed motor for rapid probe turning.

Main results.

Twister3 greatly increases the speed and repeatability of constructing twisted microwire probes compared to existing options. Users with less than one hour of experience using the device were able to make ~70 tetrodes per hour, on average. It is cheap, well documented, and all associated designs and source code are open-source.

Significance.

Twister3 significantly reduces the labor burden of creating high-quality TWPs so electrophysiologists can spend more of their time performing recordings rather than making probes. Therefore, this device is of interest to any lab performing TWP neural recordings, for example, using microdrives.

Robotic microscopy for everyone: the OpenFlexure microscope

Optical microscopes are an essential tool for both the detection of disease in clinics, and for scientific analysis. However, in much of the world access to high-performance microscopy is limited by both the upfront cost and maintenance cost of the equipment. Here we present an open-source, 3D-printed, and fully-automated laboratory microscope, with motorised sample positioning and focus control. The microscope is highly customisable, with a number of options readily available including trans- and epi- illumination, polarisation contrast imaging, and epi-florescence imaging. The OpenFlexure microscope has been designed to enable low-volume manufacturing and maintenance by local personnel, vastly increasing accessibility. We have produced over 100 microscopes in Tanzania and Kenya for educational, scientific, and clinical applications, demonstrating that local manufacturing can be a viable alternative to international supply chains that can often be costly, slow, and unreliable.

Modular assays for the quantitative study of visually guided navigation in both flying and walking flies

BACKGROUND

The quantitative study of behavioral responses to visual stimuli provides crucial information about the computations executed by neural circuits. Insects have long served as powerful model systems, either when walking on air suspended balls (spherical treadmill), or flying while glued to a needle (virtual flight arena).

NEW METHOD

Here we present detailed instructions for 3D-printing and assembly of arenas optimized for visually guided navigation, including codes for presenting both celestial and panorama cues. These modular arenas can be used either as virtual flight arenas, or as spherical treadmills and consist entirely of commercial and 3D-printed components placed in a temperature and humidity controlled environment.

COMPARISON TO EXISTING METHOD(S)

Previous assays often include a combination of rather cost-intensive and technically complex, custom-built mechanical, electronic, and software components. Implementation amounts to a major challenge when working in an academic environment without the support of a professional machine shop.

RESULTS

Robust optomotor responses are induced in flyingDrosophila by displaying moving stripes in a cylinder surrounding the magnetically tethered fly. Similarly, changes in flight heading are induced by presenting changes in the orientation of linearly polarized UV light presented from above. Finally, responses to moving patterns are induced when individual flies are walking on an air-suspended ball.

CONCLUSION

These modular assays allow for the investigation of a diverse combination navigational cues (sky and panorama) in both flying and walking flies. They can be used for the molecular dissection of neural circuitry in Drosophila and can easily be rescaled for accommodating other insects.

3D Printable Device for Automated Operant Conditioning in the Mouse

Operant conditioning (OC) is a classical paradigm and a standard technique used in experimental psychology in which animals learn to perform an action to achieve a reward. By using this paradigm, it is possible to extract learning curves and measure accurately reaction times (RTs). Both these measurements are proxy of cognitive capabilities and can be used to evaluate the effectiveness of therapeutic interventions in mouse models of disease. Here, we describe a fully 3D printable device that is able to perform OC on freely moving mice, while performing real-time tracking of the animal position. We successfully trained six mice, showing stereotyped learning curves that are highly reproducible across mice and reaching >70% of accuracy after 2 d of conditioning. Different products for OC are commercially available, though most of them do not provide customizable features and are relatively expensive. This data demonstrate that this system is a valuable alternative to available state-of-the-art commercial devices, representing a good balance between performance, cost, and versatility in its use.