Robotic microscopy for everyone: the OpenFlexure microscope

Using old laboratory equipment with modern Web-of-Things standards: a smart laboratory with LabThings Retro

There has been an increasing, and welcome, open hardware trend towards science teams building and sharing their designs for new instruments. These devices, often built upon low-cost microprocessors and microcontrollers, can be readily connected to enable complex, automated and smart experiments. When designed to use open communication web standards, devices from different laboratories and manufacturers can be controlled using a single protocol and even communicate with each other. However, science labs still have a majority of old, perfectly functional equipment which tends to use older, and sometimes proprietary, standards for communications. In order to encourage the continued and integrated use of this equipment in modern automated experiments, we develop and demonstrate LabThings Retro. This allows us to retrofit old instruments to use modern Web-of-Things standards, which we demonstrate with closed-loop feedback involving an optical microscope, digital imaging and fluid pumping.

Open instrumentation, like open data, is key to reproducible science. Yet, without incentives it won't thrive

There is far more to open science than simply not shutting away your work. For example, a significant time investment must be made to collate, curate, explain and document precisely how an experiment can be reproduced or data can be reused. This time investment is currently poorly rewarded in our current model of open science where a bare minimum of openness is mandated, but further work is not recognized. As the open science movement looks beyond open access publications and open data towards ongoing detailed work such as open source software and open source hardware, it needs to consider how to properly encourage the extra work that is needed to properly document these projects. Without detailed documentation, the work cannot be replicated, reused and continually improved. If the work cannot be replicated or reused, is it really even open? This article is part of the Theo Murphy meeting issue 'Open, reproducible hardware for microscopy'.

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.

Smartphone-based optical sectioning (SOS) microscopy with a telecentric design for fluorescence imaging

We propose a smartphone-based optical sectioning (SOS) microscope based on the HiLo technique, with a single smartphone replacing a high-cost illumination source and a camera sensor. We built our SOS with off-the-shelf optical, mechanical cage systems with 3D-printed adapters to seamlessly integrate the smartphone with the SOS main body. The liquid light guide can be integrated with the adapter, guiding the smartphone's LED light to the digital mirror device (DMD) with neglectable loss. We used an electrically tuneable lens (ETL) instead of a mechanical translation stage to realise low-cost axial scanning. The ETL was conjugated to the objective lens's back pupil plane (BPP) to construct a telecentric design by a 4f configuration to maintain the lateral magnification for different axial positions. SOS has a 571.5 µm telecentric scanning range and an 11.7 µm axial resolution. The broadband smartphone LED torch can effectively excite fluorescent polystyrene (PS) beads. We successfully used SOS for high-contrast fluorescent PS beads imaging with different wavelengths and optical sectioning imaging of multilayer fluorescent PS beads. To our knowledge, the proposed SOS is the first smartphone-based HiLo optical sectioning microscopy (£1965), which can save around £7035 compared with a traditional HiLo system (£9000). It is a powerful tool for biomedical research in resource-limited areas.

Low-cost, versatile, and highly reproducible microfabrication pipeline to generate 3D-printed customised cell culture devices with complex designs

Cell culture devices, such as microwells and microfluidic chips, are designed to increase the complexity of cell-based models while retaining control over culture conditions and have become indispensable platforms for biological systems modelling. From microtopography, microwells, plating devices, and microfluidic systems to larger constructs such as live imaging chamber slides, a wide variety of culture devices with different geometries have become indispensable in biology laboratories. However, while their application in biological projects is increasing exponentially, due to a combination of the techniques, equipment and tools required for their manufacture, and the expertise necessary, biological and biomedical labs tend more often to rely on already made devices. Indeed, commercially developed devices are available for a variety of applications but are often costly and, importantly, lack the potential for customisation by each individual lab. The last point is quite crucial, as often experiments in wet labs are adapted to whichever design is already available rather than designing and fabricating custom systems that perfectly fit the biological question. This combination of factors still restricts widespread application of microfabricated custom devices in most biological wet labs. Capitalising on recent advances in bioengineering and microfabrication aimed at solving these issues, and taking advantage of low-cost, high-resolution desktop resin 3D printers combined with PDMS soft lithography, we have developed an optimised a low-cost and highly reproducible microfabrication pipeline. This is thought specifically for biomedical and biological wet labs with not prior experience in the field, which will enable them to generate a wide variety of customisable devices for cell culture and tissue engineering in an easy, fast reproducible way for a fraction of the cost of conventional microfabrication or commercial alternatives. This protocol is designed specifically to be a resource for biological labs with limited expertise in those techniques and enables the manufacture of complex devices across the μm to cm scale. We provide a ready-to-go pipeline for the efficient treatment of resin-based 3D-printed constructs for PDMS curing, using a combination of polymerisation steps, washes, and surface treatments. Together with the extensive characterisation of the fabrication pipeline, we show the utilisation of this system to a variety of applications and use cases relevant to biological experiments, ranging from micro topographies for cell alignments to complex multipart hydrogel culturing systems. This methodology can be easily adopted by any wet lab, irrespective of prior expertise or resource availability and will enable the wide adoption of tailored microfabricated devices across many fields of biology.

Biomedical Optics Express recognizes the 2023 best paper prize winners: editorial

The Editor-in-Chief and Deputy Editor of Biomedical Optics Express announce the prize for the best paper published in the Journal between 2020 and 2022.

Utility of a Low-Cost 3-D Printed Microscope for Evaluating Esophageal Biopsies

In this manuscript we assessed the utility of a low-cost 3D printed microscope to evaluate esophageal biopsies. We conducted a comparative analysis between the traditional microscope and our 3-D printed microscope, utilizing a set of esophageal biopsy samples obtained from patients undergoing screening endoscopy. Two pathologists independently examined 30 esophageal biopsies by light microscopy and digital images obtained using a low-cost 3D printed microscope (Observer 1 and 2). The glass slide consensus diagnosis was compared to the findings of 2 additional pathologist who independently just reviewed the digital images (Observer 3 and 4). The intra-observer agreement was substantial to almost perfect for observer 1 (k:0.64) and 2 (k:0.84). All four observers had 100% sensitivity and negative predictive value, whereas specificity ranged from 59% to 100% and positive predictive value ranged from 21% to 100%. The PPV and specificity were lower for the two Observers (3 and 4) who just examined the digital images. Overall, our results suggest that telepathology may be used with high sensitivity and specificity, utilizing the pictures produced by our 3D-printed microscope.

Toward an open-source 3D-printable laboratory

Premise

Low-cost, repairable lab equipment is rare within the biological sciences. By lowering the costs of entry using 3D printing and open-source hardware, our goal is to empower both amateur and professional scientists to conduct research.

Methods

We developed a modular system of 3D-printable designs called COBLE (Collection of Bespoke Laboratory Equipment), including novel and remixed 3D-printable lab equipment that can be inexpensively printed, assembled, and repaired for a fraction of the cost of retail equivalents.

Results

Here we present novel tools that utilize 3D printing to enable a wide range of scientific experiments. We include additional resources for scientists and labs that are interested in utilizing 3D printing for their research.

Discussion

By describing the broad potential that 3D-printed designs can have in the biological sciences, we hope to inspire others to implement and improve upon these designs, improving accessibility and enabling science for all.

Utilization of accessible resources in the fabrication of an affordable, portable, high-resolution, 3D printed, digital microscope for Philippine diagnostic applications

Philippine clinical laboratory licensing requirements mandate that diagnostic microscopy for Tuberculosis (TB) sputum microscopy, urinalysis, pap smears, wet smears, an option for complete blood count, stool exams, and malaria thick and thin smears should be accessible and available in health facilities including primary care centers. However, access to these essential diagnostics is hampered by the lack of trained personnel, relatively high costs for supplies and equipment especially in rural and underserved areas. This served as motivation for our team to utilize accessible resources in the form of affordable 3D printers, available CAD software, and components to build our low-cost Openflexure microscope (OFM) prototype. We successfully fabricated our prototype for a total of 310$ with a weight of 525g. We used pathology teaching slides from the Ateneo School of Medicine and Public Health and examined the OFM prototype imaging capabilities. The calculated image resolution was 13% higher compared to an LED light microscope sample captured by a mobile phone at 40x and 15% for 100x. The sampled slide images had adequate clarity with some identifiable cellular features for Rheumatic Heart Disease (RHD), Tuberculosis in soft tissue, and Ascariasis. We were able to correct the color aberrations of the OFM we built and was able to scan images up to 1000x magnification without using oil. Given the features and cost, the OFM prototype can be an attractive and affordable option as an alternative or augmentation to diagnostic microscopy in Philippine primary care. Moreover, it may enable telepathology to support diagnostic microscopy in frontline care.

Time- and distance-resolved robotic imaging of fluid flow in vertical microfluidic strips: a new technique for quantitative, multiparameter measurement of global haemostasis

Measuring the complex processes of blood coagulation, haemostasis and thrombosis that are central to cardiovascular health and disease typically requires a choice between high-resolution low-throughput laboratory assays, or simpler less quantitative tests. We propose combining mass-produced microfluidic devices with open-source robotic instrumentation to enable rapid development of affordable and portable, yet high-throughput and performance haematological testing. A time- and distance-resolved fluid flow analysis by Raspberry Pi imaging integrated with controlled sample addition and illumination, enabled simultaneous tracking of capillary rise in 120 individual capillaries (∼160, 200 or 270 μm internal diameter), in 12 parallel disposable devices. We found time-resolved tracking of capillary rise in each individual microcapillary provides quantitative information about fluid properties and most importantly enables quantitation of dynamic changes in these properties following stimulation. Fluid properties were derived from flow kinetics using a pressure balance model validated with glycerol-water mixtures and blood components. Time-resolved imaging revealed fluid properties that were harder to determine from a single endpoint image or equilibrium analysis alone. Surprisingly, instantaneous superficial fluid velocity during capillary rise was found to be largely independent of capillary diameter at initial time points. We tested if blood function could be measured dynamically by stimulating blood with thrombin to trigger activation of global haemostasis. Thrombin stimulation slowed vertical fluid velocity consistent with a dynamic increase in viscosity. The dynamics were concentration-dependent, with highest doses reducing flow velocity faster (within 10 s) than lower doses (10-30 s). This open-source imaging instrumentation expands the capability of affordable microfluidic devices for haematological testing, towards high-throughput multi-parameter blood analysis needed to understand and improve cardiovascular health.

openFrame: A modular, sustainable, open microscopy platform with single-shot, dual-axis optical autofocus module providing high precision and long range of operation

'openFrame' is a modular, low-cost, open-hardware microscopy platform that can be configured or adapted to most light microscopy techniques and is easily upgradeable or expandable to multiple modalities. The ability to freely mix and interchange both open-source and proprietary hardware components or software enables low-cost, yet research-grade instruments to be assembled and maintained. It also enables rapid prototyping of advanced or novel microscope systems. For long-term time-lapse image data acquisition, slide-scanning or high content analysis, we have developed a novel optical autofocus incorporating orthogonal cylindrical optics to provide robust single-shot closed-loop focus lock, which we have demonstrated to accommodate defocus up to ±37 μm with <200 nm accuracy, and a two-step autofocus mode which we have shown can operate with defocus up to ±68 μm. We have used this to implement automated single molecule localisation microscopy (SMLM) in a relatively low-cost openFrame-based instrument using multimode diode lasers for excitation and cooled CMOS cameras.

Open Hardware for Microfluidics: Exploiting Raspberry Pi Singleboard Computer and Camera Systems for Customisable Laboratory Instrumentation

The integration of Raspberry Pi miniature computer systems with microfluidics has revolutionised the development of low-cost and customizable analytical systems in life science laboratories. This review explores the applications of Raspberry Pi in microfluidics, with a focus on imaging, including microscopy and automated image capture. By leveraging the low cost, flexibility and accessibility of Raspberry Pi components, high-resolution imaging and analysis have been achieved in direct mammalian and bacterial cellular imaging and a plethora of image-based biochemical and molecular assays, from immunoassays, through microbial growth, to nucleic acid methods such as real-time-qPCR. The control of image capture permitted by Raspberry Pi hardware can also be combined with onboard image analysis. Open-source hardware offers an opportunity to develop complex laboratory instrumentation systems at a fraction of the cost of commercial equipment and, importantly, offers an opportunity for complete customisation to meet the users' needs. However, these benefits come with a trade-off: challenges remain for those wishing to incorporate open-source hardware equipment in their own work, including requirements for construction and operator skill, the need for good documentation and the availability of rapid prototyping such as 3D printing plus other components. These advances in open-source hardware have the potential to improve the efficiency, accessibility, and cost-effectiveness of microfluidic-based experiments and applications.

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.

3D Printing a Low-Cost Miniature Accommodating Optical Microscope

This decade has witnessed the tremendous progress in miniaturizing optical imaging systems. Despite the advancements in 3D printing optical lenses at increasingly smaller dimensions, challenges remain in precisely manufacturing the dimensionally compatible optomechanical components and assembling them into a functional imaging system. To tackle this issue, the use of 3D printing to enable digitalized optomechanical component manufacturing, part-count-reduction design, and the inclusion of passive alignment features is reported here, all for the ease of system assembly. The key optomechanical components of a penny-sized accommodating optical microscope are 3D printed in 50 min at a significantly reduced unit cost near $4. By actuating a built-in voice-coil motor, its accommodating capability is validated to focus on specimens located at different distances, and a focus-stacking function is further utilized to greatly extend depth of field. The microscope can be readily customized and rapidly manufactured to respond to task-specific needs in form factor and optical characteristics.

A Low-Cost Modular Imaging System for Rapid, Multiplexed Immunofluorescence Detection in Clinical Tissues

To image 4-plex immunofluorescence-stained tissue samples at a low cost with cellular level resolution and sensitivity and dynamic range required to detect lowly and highly abundant targets, here we describe a robust, inexpensive (<$9000), 3D printable portable imaging device (Tissue Imager). The Tissue Imager can immediately be deployed on benchtops for in situ protein detection in tissue samples. Applications for this device are broad, ranging from answering basic biological questions to clinical pathology, where immunofluorescence can detect a larger number of markers than the standard H&E or chromogenic immunohistochemistry (CIH) staining, while the low cost also allows usage in classrooms. After characterizing our platform's specificity and sensitivity, we demonstrate imaging of a 4-plex immunology panel in human cutaneous T-cell lymphoma (CTCL) formalin-fixed paraffin-embedded (FFPE) tissue samples. From those images, positive cells were detected using CellProfiler, a popular open-source software package, for tumor marker profiling. We achieved a performance on par with commercial epifluorescence microscopes that are >10 times more expensive than our Tissue Imager. This device enables rapid immunofluorescence detection in tissue sections at a low cost for scientists and clinicians and can provide students with a hands-on experience to understand engineering and instrumentation. We note that for using the Tissue Imager as a medical device in clinical settings, a comprehensive review and approval processes would be required.

Controlling and scripting laboratory hardware with open-source, intuitive interfaces: OpenFlexure Voice Control and OpenFlexure Blockly

Making user interaction with laboratory equipment more convenient and intuitive should promote experimental work and help researchers to complete their tasks efficiently. The most common form of interaction in current instrumentation is either direct tactile, with buttons and knobs, or interfaced through a computer, using a mouse and keyboard. Scripting is another function typical of smart and automated laboratory equipment, yet users are currently required to learn bespoke programming languages and libraries for individual pieces of equipment. In this paper, we present two open-source, novel and intuitive ways of interacting with and scripting laboratory equipment. We choose the OpenFlexure family of microscopes as our exemplar, due to their open-source nature and smart control system. Firstly, we demonstrate 'OpenFlexure Voice Control' to enable users to control the microscope hands-free. Secondly, we present 'OpenFlexure Blockly' which uses the Blockly Visual Programming Language to enable users to easily create scripts for the microscope, using a drag and drop Web interface. We explain the design choices when developing these tools, and discuss more typical use cases and more general applications.

Multiple-scattering simulator-trained neural network for intensity diffraction tomography

Recovering 3D phase features of complex biological samples traditionally sacrifices computational efficiency and processing time for physical model accuracy and reconstruction quality. Here, we overcome this challenge using an approximant-guided deep learning framework in a high-speed intensity diffraction tomography system. Applying a physics model simulator-based learning strategy trained entirely on natural image datasets, we show our network can robustly reconstruct complex 3D biological samples. To achieve highly efficient training and prediction, we implement a lightweight 2D network structure that utilizes a multi-channel input for encoding the axial information. We demonstrate this framework on experimental measurements of weakly scattering epithelial buccal cells and strongly scattering C. elegans worms. We benchmark the network's performance against a state-of-the-art multiple-scattering model-based iterative reconstruction algorithm. We highlight the network's robustness by reconstructing dynamic samples from a living worm video. We further emphasize the network's generalization capabilities by recovering algae samples imaged from different experimental setups. To assess the prediction quality, we develop a quantitative evaluation metric to show that our predictions are consistent with both multiple-scattering physics and experimental measurements.

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.

Galleria mellonella immune melanization is fungicidal during infection

A key component of the insect immune response is melanin production, including within nodules, or aggregations of immune cells surrounding microbes. Melanization produces oxidative and toxic intermediates that limit microbial infections. However, a direct fungicidal role of melanin during infection has not been demonstrated. We previously reported that the fungus Cryptococcus neoformans is encapsulated with melanin within nodules of Galleria mellonella hosts. Here we developed techniques to study melanin's role during C. neoformans infection in G. mellonella. We provided evidence that in vivo melanin-encapsulation was fungicidal. To further study immune melanization, we applied tissue-clearing techniques to visualize melanized nodules in situ throughout the larvae. Further, we developed a time-lapse microscopy protocol to visualize the melanization kinetics in extracted hemolymph following fungal exposure. Using this technique, we found that cryptococcal melanin and laccase enhance immune melanization. We extended this approach to study the fungal pathogens Candida albicans and Candida auris. We find that the yeast morphologies of these fungi elicited robust melanization responses, while hyphal and pseudohyphal morphologies were melanin-evasive. Approximately 23% of melanin-encapsulated C. albicans yeast can survive and breakthrough the encapsulation. Overall, our results provide direct evidence that immune melanization functions as a direct antifungal mechanism in G. mellonella.

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.

Constructing a cost-efficient, high-throughput and high-quality single-molecule localization microscope for super-resolution imaging

Single-molecule localization microscopy (SMLM) leverages the power of modern optics to unleash ultra-precise structural nanoscopy of complex biological machines in their native environments as well as ultra-sensitive and high-throughput medical diagnostics with the sensitivity of a single molecule. To achieve this remarkable speed and resolution, SMLM setups are either built by research laboratories with strong expertise in optical engineering or commercially sold at a hefty price tag. The inaccessibility of SMLM to life scientists for technical or financial reasons is detrimental to the progress of biological and biomedical discoveries reliant on super-resolution imaging. In this work, we present the NanoPro, an economic, high-throughput, high-quality and easy-to-assemble SMLM for super-resolution imaging. We show that our instrument performs similarly to the most expensive, best-in-class commercial microscopes and rivals existing open-source microscopes at a lower price and construction complexity. To facilitate its wide adoption, we compiled a step-by-step protocol, accompanied by extensive illustrations, to aid inexperienced researchers in constructing the NanoPro as well as assessing its performance by imaging ground-truth samples as small as 20 nm. The detailed visual instructions make it possible for students with little expertise in microscopy engineering to construct, validate and use the NanoPro in <1 week, provided that all components are available.

A review on low-cost microscopes for Open Science

This article presents a review after an exhaustive search that yielded 23 works carried out in the last decade for the availability of optical microscopes with open hardware as a low-cost alternative to commercial systems. These works were developed with the aim of covering needs within several areas such as: Bio Sciences research in institutions with limited resources, diagnosis of diseases and health screenings in large populations in developing countries, and training in educational contexts with a need for high availability of equipment and low replacement cost. The analysis of the selected works allows us to classify the analyzed solutions into two main categories, for which their essential characteristics are enumerated: portable field microscopes and multipurpose automated microscopes. Moreover, this work includes a discussion on the degree of maturity of the solutions in terms of the adoption of practices aligned with the development of Open Science. RESEARCH HIGHLIGHTS: Concise review on low-cost microscopes for developing Open Science, exposing the role of smartphone-based microscopy. The work classifies microscopes in two main categories: (1) portable field microscopes, and (2) multipurpose automated microscopes.

Multidisciplinary biophotonics, open science, and … plug & pray deep learning?

Due to its great creative potential for innovation and scientific discovery, inter- and multidisciplinary collaboration is being increasingly encouraged by institutions and funding agencies. The increased opportunities in the multidisciplinary arena also come with significant challenges like the added experimental, analytical and logistical complexity, blended with a high likelihood of miscommunications. When is multidisciplinarity worth the effort, and how can we be better collaborators? With a focus on cross-disciplinary collaborative work to answer burning questions in biology and biomedicine, this paper discusses both large challenges and opportunities with multidisciplinary biophotonics, how we can better navigate the arena of big data and artificial intelligence combined with open, reproducible science and biological discoveries.

A 3D Printer in the Lab: Not Only a Toy

Although 3D printers are becoming more common in households, they are still under-represented in many laboratories worldwide and regarded as toys rather than as laboratory equipment. This short review wants to change this conservative point of view. This mini-review focuses on fused deposition modeling printers and what happens after acquiring your first 3D printer. In short, these printers melt plastic filament and deposit it layer by layer to create the final object. They are getting cheaper and easier to use, and nowadays it is not difficult to find good 3D printers for less than €500. At such a price, a 3D printer is one, if not the most, versatile piece of equipment you can have in a laboratory.

A Drop-in, Focus-Extending Phase Mask Simplifies Microscopic and Microfluidic Imaging Systems for Cost-Effective Point-of-Care Diagnostics

Microscopic imaging and imaging flow cytometry have wide potential in point-of-care assays; however, their narrow depth of focus necessitates precise mechanical or fluidic focus control of a sample in order to acquire high-quality images that can be used for downstream analysis, increasing the cost and complexity of the imaging system. This complexity represents a barrier to miniaturization and translation of point-of-care assays based on microscopic imaging or imaging flow cytometry. To address this challenge, we present a simple drop-in phase mask with a physics-informed, circularly symmetric asphere phase profile that extends the depth of focus by >5-fold while largely preserving the image quality compared to other depth extending methods. We show that such a focus-extended system overcomes manufacturing tolerances in low-cost sample chambers, enlarges the useable field-of-view of low-cost objectives, and permits increased throughput and precision in flow imaging systems without the need for complex flow-focusing. As the image quality is preserved without the need for postacquisition image restoration, our solution is also highly appropriate for on-line applications such as cell sorting.

Multi-modal microscopy imaging with the OpenFlexure Delta Stage

Microscopes are vital pieces of equipment in much of biological research and medical diagnostics. However, access to a microscope can represent a bottleneck in research, especially in lower-income countries. 'Smart' computer controlled motorized microscopes, which can perform automated routines or acquire images in a range of modalities are even more expensive and inaccessible. Developing low-cost, open-source, smart microscopes enables more researchers to conceive and execute optimized or more complex experiments. Here we present the OpenFlexure Delta Stage, a 3D-printed microscope designed for researchers. Powered by the OpenFlexure software stack, it is capable of performing automated experiments. The design files and assembly instructions are freely available under an open licence. Its intuitive and modular design-along with detailed documentation-allows researchers to implement a variety of imaging modes with ease. The versatility of this microscope is demonstrated by imaging biological and non-biological samples (red blood cells with Plasmodium parasites and colloidal particles in brightfield, epi-fluorescence, darkfield, Rheinberg and differential phase contrast. We present the design strategy and choice of tools to develop devices accessible to researchers from lower-income countries, as well as the advantages of an open-source project in this context. This microscope, having been open-source since its conception, has already been built and tested by researchers around the world, promoting a community of expertise and an environment of reproducibility in science.

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.

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.

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.

UCsim2: two-dimensionally structured illumination microscopy using UC2

State-of-the-art microscopy techniques enable the imaging of sub-diffraction barrier biological structures at the price of high costs or a lack of transparency. We try to reduce some of these barriers by presenting a super-resolution upgrade to our recently presented open-source optical toolbox UC2. Our new injection moulded parts allow larger builds with higher precision. The 4× lower manufacturing tolerance compared to three-dimensional printing makes assemblies more reproducible. By adding consumer-grade available open-source hardware such as digital mirror devices and laser projectors, we demonstrate a compact three-dimensional multimodal setup that combines image scanning microscopy and structured illumination microscopy. We demonstrate a gain in resolution and optical sectioning using the two different modes compared to the widefield limit by imaging Alexa Fluor ® 647- and Silicon Rhodamine-stained HeLa cells. We compare different objective lenses and by sharing the designs and manuals of our setup, we make super-resolution imaging available to everyone. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 2)'.

Super-resolution microscopy: a brief history and new avenues

Super-resolution microscopy (SRM) is a fast-developing field that encompasses fluorescence imaging techniques with the capability to resolve objects below the classical diffraction limit of optical resolution. Acknowledged with the Nobel prize in 2014, numerous SRM methods have meanwhile evolved and are being widely applied in biomedical research, all with specific strengths and shortcomings. While some techniques are capable of nanometre-scale molecular resolution, others are geared towards volumetric three-dimensional multi-colour or fast live-cell imaging. In this editorial review, we pick on the latest trends in the field. We start with a brief historical overview of both conceptual and commercial developments. Next, we highlight important parameters for imaging successfully with a particular super-resolution modality. Finally, we discuss the importance of reproducibility and quality control and the significance of open-source tools in microscopy. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 2)'.

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.

Democratising “Microscopi”: a 3D printed automated XYZT fluorescence imaging system for teaching, outreach and fieldwork

Commercial fluorescence microscope stands and fully automated XYZt fluorescence imaging systems are generally beyond the limited budgets available for teaching and outreach. We have addressed this problem by developing “Microscopi”, an accessible, affordable, DIY automated imaging system that is built from 3D printed and commodity off-the-shelf hardware, including electro-mechanical, computer and optical components. Our design features automated sample navigation and image capture with a simple web-based graphical user interface, accessible with a tablet or other mobile device. The light path can easily be switched between different imaging modalities. The open source Python-based control software allows the hardware to be driven as an integrated imaging system. Furthermore, the microscope is fully customisable, which also enhances its value as a learning tool. Here, we describe the basic design and demonstrate imaging performance for a range of easily sourced specimens.

Understanding immune signaling using advanced imaging techniques

Advanced imaging is key for visualizing the spatiotemporal regulation of immune signaling which is a complex process involving multiple players tightly regulated in space and time. Imaging techniques vary in their spatial resolution, spanning from nanometers to micrometers, and in their temporal resolution, ranging from microseconds to hours. In this review, we summarize state-of-the-art imaging methodologies and provide recent examples on how they helped to unravel the mysteries of immune signaling. Finally, we discuss the limitations of current technologies and share our insights on how to overcome these limitations to visualize immune signaling with unprecedented fidelity.

Can super-resolution microscopy become a standard characterization technique for materials chemistry?

The characterization of newly synthesized materials is a cornerstone of all chemistry and nanotechnology laboratories. For this purpose, a wide array of analytical techniques have been standardized and are used routinely by laboratories across the globe. With these methods we can understand the structure, dynamics and function of novel molecular architectures and their relations with the desired performance, guiding the development of the next generation of materials. Moreover, one of the challenges in materials chemistry is the lack of reproducibility due to improper publishing of the sample preparation protocol. In this context, the recent adoption of the reporting standard MIRIBEL (Minimum Information Reporting in Bio-Nano Experimental Literature) for material characterization and details of experimental protocols aims to provide complete, reproducible and reliable sample preparation for the scientific community. Thus, MIRIBEL should be immediately adopted in publications by scientific journals to overcome this challenge. Besides current standard spectroscopy and microscopy techniques, there is a constant development of novel technologies that aim to help chemists unveil the structure of complex materials. Among them super-resolution microscopy (SRM), an optical technique that bypasses the diffraction limit of light, has facilitated the study of synthetic materials with multicolor ability and minimal invasiveness at nanometric resolution. Although still in its infancy, the potential of SRM to unveil the structure, dynamics and function of complex synthetic architectures has been highlighted in pioneering reports during the last few years. Currently, SRM is a sophisticated technique with many challenges in sample preparation, data analysis, environmental control and automation, and moreover the instrumentation is still expensive. Therefore, SRM is currently limited to expert users and is not implemented in characterization routines. This perspective discusses the potential of SRM to transition from a niche technique to a standard routine method for material characterization. We propose a roadmap for the necessary developments required for this purpose based on a collaborative effort from scientists and engineers across disciplines.

Review on Additive Manufacturing of Catalysts and Sorbents and the Potential for Process Intensification

Additive manufacturing of catalyst and sorbent materials promises to unlock large design freedom in the structuring of these materials, and could be used to locally tune porosity, shape and resulting parameters throughout the reactor along both the axial and transverse coordinates. This contrasts catalyst structuring by conventional methods, which yields either very dense randomly packed beds or very open cellular structures. Different 3D-printing processes for catalytic and sorbent materials exist, and the selection of an appropriate process, taking into account compatible materials, porosity and resolution, may indeed enable unbounded options for geometries. In this review, recent efforts in the field of 3D-printing of catalyst and sorbent materials are discussed. It will be argued that these efforts, whilst promising, do not yet exploit the full potential of the technology, since most studies considered small structures that are very similar to structures that can be produced through conventional methods. In addition, these studies are mostly motivated by chemical and material considerations within the printing process, without explicitly striving for process intensification. To enable value-added application of 3D-printing in the chemical process industries, three crucial requirements for increased process intensification potential will be set out: i) the production of mechanically stable structures without binders; ii) the introduction of local variations throughout the structure; and iii) the use of multiple materials within one printed structure.

Robotic and Microrobotic Tools for Dental Therapy

Robotic and microrobotic tools such as dental operating microscopes and dental endoscopes are being used extensively in dental therapy, which have a significant impact on dental therapy and education. Herein, this paper reviews the state of the art of robotic and microrobotic tools for dental therapy. This article starts with a brief introduction of current robotic and microrobotic tools for dental therapy and then displays their applications in various dental problems; strengths and weaknesses are also surveyed. Lastly, the conclusion and outlook are discussed, referring to the emerging dental clinic problems and demands. This review is expected to provide guidelines for the therapeutic application of robotic and microrobotic tools and to promote the development of robots in dentistry.

Handheld and Cost-Effective Fourier Lightfield Microscope

In this work, the design, building, and testing of the most portable, easy-to-build, robust, handheld, and cost-effective Fourier Lightfield Microscope (FLMic) to date is reported. The FLMic is built by means of a surveillance camera lens and additional off-the-shelf optical elements, resulting in a cost-effective FLMic exhibiting all the regular sought features in lightfield microscopy, such as refocusing and gathering 3D information of samples by means of a single-shot approach. The proposed FLMic features reduced dimensions and light weight, which, combined with its low cost, turn the presented FLMic into a strong candidate for in-field application where 3D imaging capabilities are pursued. The use of cost-effective optical elements has a relatively low impact on the optical performance, regarding the figures dictated by the theory, while its price can be at least 100 times lower than that of a regular FLMic. The system operability is tested in both bright-field and fluorescent modes by imaging a resolution target, a honeybee wing, and a knot of dyed cotton fibers.

autohaem: 3D printed devices for automated preparation of blood smears

The process of making blood smears is common in both research and clinical settings for investigating the health of blood cells and the presence of blood-borne parasites. It is very often carried out manually. We focus here on smears for malaria diagnosis and research, which are frequently analyzed by optical microscopy and require a high quality. Automating the smear preparation promises to increase throughput and to improve the quality and consistency of the smears. We present here two devices (manual and motorized) designed to aid in the making of blood smears. These are fully documented, open-source hardware, and an important principle was to make them easily fabricated locally anywhere. Designs and assembly instructions are freely available under an open license. We also describe an image analysis pipeline for characterizing the quality of smears and use it to optimize the settings and tunable parameters in the two devices. The devices perform as well as expert human operators while not requiring a trained operator and offering potential advantages in reproducibility and standardization across facilities.

Low-cost and cleanroom-free prototyping of microfluidic and electrochemical biosensors: Techniques in fabrication and bioconjugation

Integrated microfluidic biosensors enable powerful microscale analyses in biology, physics, and chemistry. However, conventional methods for fabrication of biosensors are dependent on cleanroom-based approaches requiring facilities that are expensive and are limited in access. This is especially prohibitive toward researchers in low- and middle-income countries. In this topical review, we introduce a selection of state-of-the-art, low-cost prototyping approaches of microfluidics devices and miniature sensor electronics for the fabrication of sensor devices, with focus on electrochemical biosensors. Approaches explored include xurography, cleanroom-free soft lithography, paper analytical devices, screen-printing, inkjet printing, and direct ink writing. Also reviewed are selected surface modification strategies for bio-conjugates, as well as examples of applications of low-cost microfabrication in biosensors. We also highlight several factors for consideration when selecting microfabrication methods appropriate for a project. Finally, we share our outlook on the impact of these low-cost prototyping strategies on research and development. Our goal for this review is to provide a starting point for researchers seeking to explore microfluidics and biosensors with lower entry barriers and smaller starting investment, especially ones from low resource settings.

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.

Simplifying the OpenFlexure microscope software with the web of things

We present the OpenFlexure Microscope software stack which provides computer control of our open source motorised microscope. Our diverse community of users needs both graphical and script-based interfaces. We split the control code into client and server applications interfaced via a web API conforming to the W3C Web of Things standard. A graphical interface is viewed either in a web browser or in our cross-platform Electron application, and gives basic interactive control including common operations such as Z stack acquisition and tiled scanning. Automated control is possible from Python and Matlab, or any language that supports HTTP requests. Network control makes the software stack more robust, allows multiple microscopes to be controlled by one computer, and facilitates sharing of equipment. Graphical and script-based clients can run simultaneously, making it easier to monitor ongoing experiments. We have included an extension mechanism to add functionality, for example controlling additional hardware components or adding automation routines. Using a Web of Things approach has resulted in a user-friendly and extremely versatile software control solution for the OpenFlexure Microscope, and we believe this approach could be generalized in the future to make automated experiments involving several instruments much easier to implement.

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.

Fast, high-precision autofocus on a motorised microscope: Automating blood sample imaging on the OpenFlexure Microscope

The OpenFlexure Microscope is a 3D-printed, low-cost microscope capable of automated image acquisition through the use of a motorised translation stage and a Raspberry Pi imaging system. This automation has applications in research and healthcare, including in supporting the diagnosis of malaria in low-resource settings. The plasmodium parasites that cause malaria require high magnification imaging, which has a shallow depth of field, necessitating the development of an accurate and precise autofocus procedure. We present methods of identifying the focal plane of the microscope, and procedures for reliably acquiring a stack of focused images on a system affected by backlash and drift. We also present and assess a method to verify the success of autofocus during the scan. The speed, reliability and precision of each method are evaluated, and the limitations discussed in terms of the end users' requirements.

miniSPIM-A Miniaturized Light-Sheet Microscope

The miniSPIM is a miniaturized light-sheet microscope that enables imaging with optical sectioning on mobile camera devices such as smartphones and single-board computers. Applications of the miniSPIM include biosensing, field research, and education where maximum portability and robustness, low power consumption, and low cost are key. Here, it is shown how all of the components of a simple light-sheet microscope can be integrated within a footprint smaller than the average smartphone. Example applications include the quantification of the motion of microparticles and bacteria in fluids, the characterization of solvent polarity based on spectral shifts of the lipid probe Nile Red, and three-dimensional (3D) and time-lapse autofluorescence imaging of a live zebrafish embryo.

Optical mesoscopy, machine learning, and computational microscopy enable high information content diagnostic imaging of blood films

Automated image-based assessment of blood films has tremendous potential to support clinical haematology within overstretched healthcare systems. To achieve this, efficient and reliable digital capture of the rich diagnostic information contained within a blood film is a critical first step. However, this is often challenging, and in many cases entirely unfeasible, with the microscopes typically used in haematology due to the fundamental trade-off between magnification and spatial resolution. To address this, we investigated three state-of-the-art approaches to microscopic imaging of blood films which leverage recent advances in optical and computational imaging and analysis to increase the information capture capacity of the optical microscope: optical mesoscopy, which uses a giant microscope objective (Mesolens) to enable high-resolution imaging at low magnification; Fourier ptychographic microscopy, a computational imaging method which relies on oblique illumination with a series of LEDs to capture high-resolution information; and deep neural networks which can be trained to increase the quality of low magnification, low resolution images. We compare and contrast the performance of these techniques for blood film imaging for the exemplar case of Giemsa-stained peripheral blood smears. Using computational image analysis and shape-based object classification, we demonstrate their use for automated analysis of red blood cell morphology and visualization and detection of small blood-borne parasites such as the malarial parasite Plasmodium falciparum. Our results demonstrate that these new methods greatly increase the information capturing capacity of the light microscope, with transformative potential for haematology and more generally across digital pathology. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.

PUMA - An open-source 3D-printed direct vision microscope with augmented reality and spatial light modulator functions

3D-printed microscopes are a topical emerging field in the literature. However most microscopes presented to date are quite novel re-imaginings of the microscope's mechanical design and they are either solely dependent on, or primarily geared towards, camera-based observations rather than ergonomic direct vision screening through an ocular lens. The reliance on camera, computer and monitor for observation introduces a compromise between portability, cost and the quality of an instant wide field of view. In this report, I introduce the Portable Upgradeable Modular and Affordable (PUMA) microscope which is an open-source 3D-printed multimodality microscope that employs a traditional upright design for ease of human direct visual observations and slide screening. PUMA uses standard RMS or C-mount objectives, with a tube length 160 mm, 170 mm or infinity and wide field high eye point ocular lenses. PUMA can use simple mirror-based illumination or can be configured to a full Köhler system with Abbe condenser for high numerical aperture observations including oil immersion. PUMA also has advanced digital/optical imaging features such as a digital spatial light modulator and - unique to any 3D printed microscope to date - an augmented reality heads-up display for interactive calibrated measurements. Digital camera imaging can also be used with PUMA - in fact PUMA can take up to three separate digital cameras simultaneously. PUMA can also function as a direct vision multi-header microscope for teaching or discussion. The illumination system is also modular and includes transillumination, epi-illumination, fluorescence, polarisation, dark ground and also Schlieren-based phase contrast and other Fourier optics filtering modalities. All these advanced features are available through an on-board, battery operated, microprocessor so no mains supply, smartphone, network connection, PC or external monitor are required making PUMA a truly portable system suitable for remote field work.

Democratising "Microscopi": a 3D printed automated XYZT fluorescence imaging system for teaching, outreach and fieldwork

Commercial fluorescence microscope stands and fully automated XYZt fluorescence imaging systems are generally beyond the limited budgets available for teaching and outreach. We have addressed this problem by developing "Microscopi", an accessible, affordable, DIY automated imaging system that is built from 3D printed and commodity off-the-shelf hardware, including electro-mechanical, computer and optical components. Our design features automated sample navigation and image capture with a simple web-based graphical user interface, accessible with a tablet or other mobile device. The light path can easily be switched between different imaging modalities. The open source Python-based control software allows the hardware to be driven as an integrated imaging system. Furthermore, the microscope is fully customisable, which also enhances its value as a learning tool. Here, we describe the basic design and demonstrate imaging performance for a range of easily sourced specimens.