eduSPIM: Light Sheet Microscopy in the Museum

Successful 3D imaging of cleared biological samples with light sheet fluorescence microscopy

In parallel with the development of tissue-clearing methods, over the last decade, light sheet fluorescence microscopy has contributed to major advances in various fields, such as cell and developmental biology and neuroscience. While biologists are increasingly integrating three-dimensional imaging into their research projects, their experience with the technique is not always up to their expectations. In response to a survey of specific challenges associated with sample clearing and labeling, image acquisition, and data analysis, we have critically assessed the recent literature to characterize the difficulties inherent to light sheet fluorescence microscopy applied to cleared biological samples and to propose solutions to overcome them. This review aims to provide biologists interested in light sheet fluorescence microscopy with a primer for the development of their imaging pipeline, from sample preparation to image analysis. Importantly, we believe that issues could be avoided with better anticipation of image analysis requirements, which should be kept in mind while optimizing sample preparation and acquisition parameters.

Time to Upgrade: A New OpenSPIM Guide to Build and Operate Advanced OpenSPIM Configurations

OpenSPIM is an Open Access platform for Selective Plane Illumination Microscopy (SPIM) and allows hundreds of laboratories around the world to generate and process light-sheet data in a cost-effective way due to open-source hardware and software. While setting up a basic OpenSPIM configuration can be achieved expeditiously, correctly assembling and operating more complex OpenSPIM configurations can be challenging for routine standard OpenSPIM users. Detailed instructions on how to equip an OpenSPIM with two illumination sides and two detection axes (X-OpenSPIM) are provided, and a solution is also provided on how the temperature can be controlled in the sample chamber. Additionally, it is demonstrated how to operate it by implementing an ArduinoUNO microcontroller and introducing μOpenSPIM, a new software plugin for OpenSPIM, to facilitate image acquisition. The new software works on any OpenSPIM configuration comes with drift correction functionality, on-the-fly image processing, and gives users more options in the way time-lapse movies are initially set up and saved. Step-by-step guides are also provided within the Supporting Information and on the website on how to align the lasers, configure the hardware, and acquire images using μOpenSPIM. With this, current OpenSPIM users are empowered in various ways, and newcomers striving to use more advanced OpenSPIM systems are helped.

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.

Compact and reflective light-sheet microscopy for long-term imaging of living embryos

The development of light-sheet fluorescence microscopy has been a revolution for developmental biology as it allows long-term imaging during embryonic development. An important reason behind the quick adoption has been the availability of open hardware alternatives. In this work, we present a robust and compact version of a light-sheet fluorescence microscope that is easy to assemble and requires little to no maintenance. An important aspect of the design is that the illumination unit consists of reflective elements, thereby reducing chromatic aberrations an order of magnitude as compared to refractive counterparts.

A high-throughput and open-source platform for embryo phenomics

Phenomics has the potential to facilitate significant advances in biology but requires the development of high-throughput technologies capable of generating and analysing high-dimensional data. There are significant challenges associated with building such technologies, not least those required for investigating dynamic processes such as embryonic development, during which high rates of temporal, spatial, and functional change are inherently difficult to capture. Here, we present EmbryoPhenomics, an accessible high-throughput platform for phenomics in aquatic embryos comprising an Open-source Video Microscope (OpenVIM) that produces high-resolution videos of multiple embryos under tightly controlled environmental conditions. These videos are then analysed by the Python package Embryo Computer Vision (EmbryoCV), which extracts phenomic data for morphological, physiological, behavioural, and proxy traits during the process of embryonic development. We demonstrate the broad-scale applicability of EmbryoPhenomics in a series of experiments assessing chronic, acute, and multistressor responses to environmental change (temperature and salinity) in >30 million images of >600 embryos of two species with markedly different patterns of development—the pond snail Radix balthica and the marine amphipod Orchestia gammarellus. The challenge of phenomics is significant but so too are the rewards, and it is particularly relevant to the urgent task of assessing complex organismal responses to current rates of environmental change. EmbryoPhenomics can acquire and process data capturing functional, temporal, and spatial responses in the earliest, most dynamic life stages and is potentially game changing for those interested in studying development and phenomics more widely.

EmbryoPhenomics is an open-source technology platform for high-throughput phenome screening of aquatic embryos. This paper demonstrates its application in experiments assessing the sensitivity of aquatic embryos to environmental stress, consisting of more than 600 embryos and more than 30 million images.

Phenomics is the collection of high-dimensional phenotypic data on an organism-wide scale, and it requires high-throughput technologies. However, a lack of technologies for efficiently visualising and measuring whole-organism responses to different environments represents a serious challenge for biologists. This challenge is most apparent when studying complex responses, such as those occurring during the dynamic period of embryonic development, when the phenotype changes markedly through time. Here, we present EmbryoPhenomics (www.embryophenomics.org), a new open-source technological platform comprising high-throughput bioimaging hardware that produces high-resolution video of multiple, developing embryos maintained under controlled environmental conditions and software for automatically quantifying embryo responses from these videos. We demonstrate the broad applicability of EmbryoPhenomics using four experiments assessing responses to global change (elevated temperature and salinity) in which we generate data for more than 600 embryos produced from video comprising more than 30 million images. EmbryoPhenomics was used to capture functional, temporal, and spatial change in morphological, physiological, and behavioural responses in the earliest, most dynamic life stages and addresses a serious bottleneck in biology. Such capabilities are urgently required, particularly within the context of assessing the response of embryos to the current unprecedented rates of global environmental change.

Software Framework for Controlling Unsupervised Scientific Instruments

Science outreach and communication are gaining more and more importance for conveying the meaning of today’s research to the general public. Public exhibitions of scientific instruments can provide hands-on experience with technical advances and their applications in the life sciences. The software of such devices, however, is oftentimes not appropriate for this purpose. In this study, we describe a software framework and the necessary computer configuration that is well suited for exposing a complex self-built and software-controlled instrument such as a microscope to laymen under limited supervision, e.g. in museums or schools. We identify several aspects that must be met by such software, and we describe a design that can simultaneously be used to control either (i) a fully functional instrument in a robust and fail-safe manner, (ii) an instrument that has low-cost or only partially working hardware attached for illustration purposes or (iii) a completely virtual instrument without hardware attached. We describe how to assess the educational success of such a device, how to monitor its operation and how to facilitate its maintenance. The introduced concepts are illustrated using our software to control eduSPIM, a fluorescent light sheet microscope that we are currently exhibiting in a technical museum.