The University of Bath Multi-user Light Sheet Fluorescence Microscopy

Lead Research Organisation: University of Bath


We wish to add an important cutting-edge instrument to the University of Bath's microscopy facilities. Many aspects of physiology, cell and developmental biology are dynamic, including those on second (e.g. heart-beat), minute (e.g. cell migration) and hour or even day timescales (e.g. embryonic development and plant growth). Likewise, biological systems are frequently 3-dimensional, with structural arrangements being integral to their function (e.g. cardiovascular systems, brain, embryos). Thus, to study biological processes in detail, we need microscopy that can allow us to image biological processes on this range of timescales, and in intact 3-D samples (whole organisms, or tissues). A new technique, Light Sheet Fluorescent Microscopy (LSFM), allows all of these and promises to revolutionise these areas. Key aspects of the LSFM design ensure fast imaging, so that changes on time-scales of seconds-minutes can be resolved; gentle imaging, so that specimens are not damaged over long-term study for minutes, hours or even days; and deeper imaging, so that thicker specimens and whole living organisms become accessible. It means that we can study changes in response to drugs or pathogens over long timescales; that we can monitor cells as they migrate through complex tissues or even whole organisms, detecting changes in their behaviour as their environment alters; and that we can study processes in living cells organised into 3-D structures that more accurately mimic a physiological environment. In Bath, we propose using the LSFM for seven initial projects, each utilising one or more key features of LSFM: to study stem cells in developing zebrafish embryos, fat development in mouse models of body mass control, cell environment on cartilage properties, how bacterial communities (biofilms) become more efficient at evading antibiotic treatment, plant root responses to infection, how to make reproducible organoid cultures, and mapping neuronal activation in mouse brains. The instrument will be integrated into the Microscopy and Analysis Suite in the University of Bath, ensuring expert user training and equipment support. It will support a broad, interdisciplinary research community within the University of Bath and our collaborator institutions/organisations.

Technical Summary

We wish to expand the state-of-the-art microscopy facilities at the University of Bath by acquiring a highly capable, but user-friendly Light Sheet Fluorescent Microscope (LSFM). Modern biological studies must take account of the timescales (seconds-days) of physiological, cellular and developmental processes, and of the 3-D organisation of organisms and tissues (often, micrometre-centimetre scales). The LSFM allows imaging on these temporal and spatial scales, and is ideally suited to prolonged timelapse of living organisms, e.g. zebrafish and Arabidopsis roots, and 3-D cultures (organoids and spheroids). The approach is further enhanced when combined with new clearing approaches, allowing significant tissue/organ samples (e.g. mouse brains) to be imaged intact at high resolution. An instrument capable of all these In Bath, the team of applicants will use the LSFM to investigate stem cell and adipose tissue development, antibiotic resistance in biofilms, plant responses to pathogen infection, and neuronal activation in mouse brains, and to develop reproducible organoid culture processes. The integration of the LSFM into the Microscopy and Analysis Suite at the University of Bath, will ensuring expert equipment support and maintenance and user training. It will support a broad, interdisciplinary research community within the University of Bath and our collaborator institutions/organisations.

Planned Impact

Provision of Light Sheet Fluorescent Microscopy to the University of Bath will enable numerous multi-disciplinary studies in biosciences and bioengineering, as witnessed by the diversity of initial projects and breadth of user community brought together by this bid. These will in turn impact upon the competitiveness of the UK research base, and so to the UK knowledge economy. Our proposal aligns most closely to the BBSRC's 'Healthy ageing across the lifecourse', 'Technology development for the biosciences', 'Sustainably enhancing agricultural production' and 'Combatting microbial resistance' strategic priority areas, but also concerns 'Food, nutrition and health', 'International Partnerships', 'Reducing waste in the food chain', and 'Welfare of managed animals'. By providing novel imaging capability, the user consortium will be able to be able to investigate their model systems in ways allowing direct observation of dynamic processes and 3-D structures on scales outside of current capability. These observations will then have direct application to the strategic priority areas listed.
Our work will have significant impact on 1) the academic community by allowing them to study living, 3-D models with much greater physiological relevance; 2) the private sector, including charities and pharmaceutical companies by developing new assays and new insights into biology, for example of drug resistance in tumours and biofilms; 3) skills training of post-graduate and post-doctoral researchers, enhancing their employability in academe, industry and elsewhere; 4) inter-disciplinary research, including mathematical biology which will be enhance by the quantitative data that may be extracted from LSFM data-sets.
The data produced by the LSFM will often be best-presented as movies, and consequently they are often readily accessible to the public, not to mention exciting to watch. Our BBSRC ALERT18 bid will be announced to the public and research outputs disseminated through a range of public engagement activities.


10 25 50
Description The impacts of COVID in 2020 and 2021 profoundly affected our opportunities to utilise the Light Sheet Microsocpe purchased under this award. Lockdowns and the return to work under COVID rules meant that the microscope was installed but remained unsupported for a time due to furlough arrangements and then the ongoing impacts of COVID meant that labs focused on their core research, disrupting their ability to experiment with the microscope. In one case, an PhD student did some initial experiments in early 2020, but then they were unable to do further work due to the effects of COVID pandemic before their funding expired in autumn 2020. Unfortunately, the ongoing pandemic meant that opportunities for most groups to use the microscope have been severely limited in 2021 too, but work has now begun and is expected to increase as work returns to normal.
Exploitation Route Too early
Sectors Other

Description Steffen Scholpp 
Organisation University of Exeter
Department Living Systems Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution Steffen and I have a shared BBSRC-funded PhD student, who has begun to use the Light Sheet Microscope for looking at the possible role of cytonemes in communicating Wnt signals to neural crest cells. Our acquisition of the lIght sheet microscope under this grant was crucial for this. We also have provided the key transgenic line to label the neural crest cells for imaging.
Collaborator Contribution Steffen's group have provided the tools which we expect will enable us to manipulate Wnt signalling in neural crest cells for future studies.
Impact Too early
Start Year 2021