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Leo Morgan
Leo Morgan

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From office software to mobile apps to supply chain, code vulnerabilities present an enticing opportunity for bad actors to gain access to private personal and business information by taking advantage of vulnerabilities in communication, file transfer, CI/CD and the DevOps process.


Agility and speed are crucial to the CI/CD process. But so is security. Without the right tools and implementation for best practices for signing, your code, software, and apps are vulnerable to attack.


Light microscopy enables researchers to observe cellular mechanisms with high spatial and temporal resolution. However, the increasing complexity of current imaging technologies, coupled with financial constraints of potential users, hampers the general accessibility and potential reach of cutting-edge microscopy. Open microscopy can address this issue by making well-designed and well-documented hardware and software solutions openly available to a broad audience. In this Comment, we provide a definition of open microscopy and present recent projects in the field. We discuss current and future challenges of open microscopy and their implications for funders, policymakers, researchers and scientists. We believe that open microscopy requires a holistic approach. Sample preparation, designing and building of hardware components, writing software, data acquisition and data interpretation must go hand in hand to enable interdisciplinary and reproducible science to the benefit of society.


Light microscopy has been pivotal in the life sciences to study small features and objects otherwise hidden to the naked eye. Simple microscopes such as the US$2 Foldscope or smartphone auxiliary lenses are forming the basis of citizen science projects, scientific education and medical diagnosis4,5. Driven by a societal and academic shift toward open science and technology, more and more information on advanced microscopy has become publicly available6. Although open software can be downloaded directly, the development of open hardware accelerated only recently with the increasing accessibility and affordability of suitable hardware components. With low-cost three-dimensional (3D) printers, rapid reproduction of designs and prototyping moved from professional machine shops to the hobby room. Designs milled from solid aluminum are ordered via web shops and delivered within days. Mass-produced electronics such as light-emitting or laser diodes, microcontrollers, lenses and industrial cameras have further reduced the costs and time requirements of building complex instrumentation. Scientific-grade components such as laser engines, objectives and low-noise cameras have been successfully replaced by cheaper alternatives7,8,9,10.


Even for specialist labs, implementing hardware-based imaging modalities that are published without sufficient documentation requires extensive reverse engineering and tinkering instead of waiting for commercial suppliers to implement new modalities. While commercial microscopes feature safety measures, warranty and further support, many contain proprietary information with specific internal settings and characteristics that remain unknown to the user. Open microscopy can overcome this problem by ensuring that any new method, both hardware and software, is sufficiently documented and open to allow straightforward implementation and replication. In this process, the sharing of materials or information between two or more parties should not be hindered by restrictive material transfer/non-disclosure agreements. For open hardware, recent work highlights general opportunities and best practices11,12. For light microscopy, this can include documenting the assembly and manufacturing and providing guides, a bill of materials and video tutorials.


Until recently, microscopy hardware developers seeking to develop optical methods faced the choice of either retrofitting new hardware onto an existing commercial microscope or designing and building an entire bespoke microscope from individual components. Monolithic, commercial bodies offer a stable mechanical base and are designed to minimize optical aberrations. Critical optical planes or individual optical components (mirrors, lenses), however, are not easily accessible. Features implemented for user friendliness and safety (eyepieces, safety interlocks, dedicated software) further limit developers from modifying a setup. Fully customized microscopy designs, on the other hand, offer wider control and more accessibility, but come with their own caveats. Developing new hardware can take a lot of time, especially when used on re-implementing basic components and features such as focusing or sample positioning. Moreover, custom microscopy solutions are often less user friendly compared to commercial counterparts that offer streamlined software solutions for both data acquisition and data analysis.


For researchers interested in volumetric imaging, the OpenSPIM (SPIM: selective plane illumination microscopy) project enabled many labs to build, apply and teach light-sheet microscopy at a time when commercial solutions were neither accessible nor affordable27. Similarly, the mesoSPIM initiative provides comprehensive open-source documentation28 and detailed protocols for tissue clearing29. Further, SOPi microscopy (SOPi: scanned oblique plane illumination) was introduced and features open-hardware assembly, an alignment protocol and control software for single-objective light-sheet microscopy30.


Python-based software solutions for image processing41,42,43,44 and image acquisition are prospectively enriching the long-dominant JAVA-based programs ImageJ45/Fiji46 and µManager47. The manufacturer- and platform-independent file format of the Open Microscopy Environment initiative48 ensures long-term data compatibility, for example, in the growing field of deep learning for image-quality improvements, segmentation and overall data analysis (for example, CARE49, StarDist50, CellPose51, QuPath52 and ZeroCostDL4Mic53) as recently discussed13,54,55.


With the number of hardware and software frameworks rapidly increasing, new challenges arise as potential users might feel overwhelmed by the number of available options. An illustrative example of proliferation is the variety of software packages available for data analysis in single-molecule localization microscopy. Here, the curated evaluation of more than 30 different software packages using a diverse set of metrics highlighted the benefits of open microscopy56. Open packages can be directly compared by everyone, helping end users to freely choose data analysis software that is optimal for their environment in terms of accuracy, speed, robustness, reliability and user-friendliness. We conclude that proliferation should be seen as an opportunity rather than a threat, pointing to a recent series of documents on the implementation of standards in open hardware and software development57 as well as data provenance and quality control in microscopy58,59,60,61. We suggest that these best practices are requested and followed by scientists, reviewers and editors to enable long-lasting device interoperability.


Whereas many file formats for storing and analyzing images are open and suitable viewers are freely available, this is not necessarily the case for hardware designs that feature computer-aided design (CAD)62. For 3D printing, 3D models exported in the *.stl format describe only the surface geometry of a 3D object without any scale, thereby inhibiting any modifications to the design. Alternatives, such as sharing links to cloud-based CAD software (for example, Fusion360 or Tinkercad), or relying on open-source CAD models (for example, openSCAD or FreeCAD), can help to distribute design files across different development environments. Ultimately, publishers and developers should ensure that design files are available in formats as proposed by the open-source hardware association ( -best-practices/).


The close connection between open hardware and software is inevitable for complex microscopy projects. Projects such as µManager47, Pycro-Manager41 and Python microscopy42,63 have been playing a key role in connecting setup control, data acquisition and data analysis. When it comes to hardware control, the availability of open-source device drivers and adapters is crucial. The software architecture used in µManager47, for example, standardizes how hardware devices can be controlled from diverse software components via a plugin mechanism, making it easier for developers to contribute plugins. As a case in point, the µManager community managed to collect hundreds of device adapters ( -manager.org/Device_Support).


For the primary developer, providing this kind of service, while also managing the contributions of others, comes at substantial costs, which are often difficult to cover in the current academic incentive system and so generate a strain, especially on smaller labs. Although funding bodies such as the US National Science Foundation, US National Institutes of Health, Wellcome Trust, and Max Planck Society now widely propagate the idea of open science, institutional support or open calls that are explicitly dedicated to the development and continuation of open hardware, software and knowledge exchange projects are still rare. The Chan Zuckerberg Initiative and NASA are notable exceptions that provide substantial funding to support open science. We urge policy makers and funders to set up additional funding schemes to support new, as well as existing, open-microscopy projects. Many projects will benefit from small grants ($25,000), for example, to design injection molds for the UC2 system to produce mounting cubes (Fig. 2b). Larger grants could be used to hire programmers to increase both functionality and accessibility of popular software packages. In addition to the direct funding of projects, we further highlight the importance of making 3D printers, computer numerical control (CNC) machines and general know-how on electronics or mechanical and optical engineering available at universities and other knowledge institutions. Local workshops are perfectly suited for the task of maintaining knowledge and expertise. 041b061a72


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