An upright confocal microscope for multidisciplinary research

Lead Research Organisation: University of Manchester
Department Name: School of Biological Sciences


The desire to visualise cellular structures and processes has been a central aim of biologists ever since the development of the light microscope and the advances in cell biology are intrinsically linked to the advances in microscope technology. The development of synthetic fluorescent probes made it possible to visualize the location of individual proteins and complexes within the cell and the development of different coloured probes allowed multiple proteins to be studied at the same time. This gives an insight not only into the localization of the proteins within the cell but also their interactions with other proteins. Along with this, the development of the laser scanning confocal microscope, using a detection pinhole to reject out of focus light, allowed researchers to see these fluorescent probes inside thick samples and obtain a "free from blur" optical section and three-dimensional model of the sample.

The ability to visualize protein dynamics in live cells was made possible with the discovery and subsequent sequencing of the green fluorescent protein from jelly fish. Using genetic engineering it is possible to form a protein chimera in which a protein of interest is fused to this fluorescent protein. The now fluorescently tagged protein of interests can then be expressed and observed in live cells. With the development of coloured variants of the jelly fish protein (and coral proteins), it has become possible to follow multiple different proteins inside living cells, tissues and even whole organism and has allowed researchers to use optical approaches to gain an understanding of how proteins interact, how cells communicate and how cells and tissues react to the their external environment.

Microscopes can come as essentially two models with respect to access to the sample to be imaged. An inverted model accesses the sample plated in dishes from the bottom and high resolution imaging needs imaging through thin transparent surfaces such as glass. An upright microscope accesses samples placed in dishes directly from the top with the use of lenses that can be "dipped" (hence dipping lenses) in the culture media. The use of this approach enables imaging of samples without additional interface which can be thick or opaque etc. Such approach allows imaging of samples that grow in a three-dimensional environment resembling their natural in vivo environment. Such environments can be original tissue or in-vivo like engineered biomaterials. These new developments provide a realistic insight into the role of how cells behave in their environment in health and disease, and an upright confocal microscope provides the ideal platform and critical for imaging cells under such modified environments.

Whist we currently have a Leica SP5 upright confocal microscope, it is at the end of its useful life and lacks sensitivity which is critical for imaging combined with new other technologies such as CRISPR, where single copies of fluorescently labelled protein genes are targeted to specific locations within the genome of cells and organisms. Although this targeted approach offers enormous potential for understanding the role of individual proteins in the cell, their level of expression is often so low that the resulting fluorescent signal is very weak. The latest generation of upright confocal microscopes provide the ability to perform these sophisticated multi-colour microscope experiments even on thick samples due to their improved light efficiency and detector sensitivity.

Here we propose to replace our old out-dated upright microscope with a new state-of-the-art Leica SP8 upright confocal microscope. This will allow improved delivery of a core service to a productive set of around 67 well-funded research groups who heavily use the current instrument and will provide them with access to a system with improved flexibility, improved sensitivity and improved resolution.

Technical Summary

The existing Leica SP5 upright confocal in the Faculty of Biology Medicine and Health is heavily utilised but it is out-dated. Sample thickness, dimensionality or opaqueness often requires direct optical access to the sample and this is not possible on existing inverted microscopes. As the use of samples embedded in bio-materials and tissues increases, so does the demand for access to a state-of-the-art upright confocal system.

To meet this demand we propose the purchase of a new Leica SP8 upright confocal system equipped with a tunable white light laser, dipping objectives, spectral imaging, the latest hybrid (HyD) detectors and triggering of ancillary components. The tunable white light laser and spectral detection sliders allows the excitation and emission wavelengths to be matched exactly to that of any fluorophore, while the hybrid (HyD) detectors are twice as sensitive as traditional PMT detectors. These optical advances are increasingly important as we use technologies such as CRISPR to label single copies of endogenous genes, resulting in lower fluorescent signals, as well as the need for better multiplexing and spectral discrimination.
The dipping objectives provide direct optical access to cells in three-dimensional tissues and substrates and will also enable us to image cleared tissue, a technology that is gaining interest and already used with light sheet microscopy in Manchester. A significant group of users require the use of the upright confocal along with ancillary equipment such as fluidic devices and force measurement on custom-made stages.

This upright confocal will support a wide range of interdisciplinary science that lies within the BBSRC remit. Supporting this, the group of applicants and users of the microscope have more than 30 current BBSRC grants and >£50m current funding. Work on the microscope will span from bacteria, zebra fish, Caenorrhabditis and Drosophila model systems through to mouse and human cells and tissues.

Planned Impact

This application requests an upright confocal microscope that will support the research of a large number of users whose projects address biological, physical, and medical questions. Thus, there are a wide range of direct and indirect beneficiaries of this research:

(1) Biotechnology. The data resulting from the use of the microscope contributes to the research that will reach a broad audience across disciplines including biomedical sciences, biophysics and tissue engineering. Such research automatically leads to the development of Biotechnological tools. Tools will range from cell lines stably expressing fluorophore-tagged proteins (that may become valuable for the screening of materials and drugs affecting cellular behaviour) to the development of new reagents and devices that promote imaging or other methodologies. We expect a high potential impact in the biotechnology area and will actively search for relevant systems/companies to share our knowledge. The impact will be direct and mid-term.

(2) Pharmaceutical industry. A number of projects in the Faculty relate to cell behaviour under changing mechanical and biochemical environments. Unravelling the mechanisms through imaging will provide a starting point for the development of pharmaceutical products influencing cellular responses to changing environments in healthy or diseased tissue. Modulating cell responses to changing properties is designed to promote regeneration. The new Faculty structure will support this undertaking. The impact will be direct and mid- to long-term.

(3) General public. Images generated from this project are colourful, intuitive, attractive and make science more accessible. They are useful for educating the public, and particularly children through school lectures, about science. As a nexus between different types of research the Bioimaging Facility will help focus on how disciplines can be integrated to deliver tangible benefits for society, in terms of finding new ways to understand and treat disease as well as to develop new material. Promoting health processes will improve life quality of thousands of people in the UK and beyond the borders. Furthermore, it will drastically reduce treatment costs, thus directly and indirectly impacting the healthcare system. The impact is indirect and can range from short- to long-term.

(4) Researchers of various backgrounds. The Bioimaging Facility with its imaging tools being key for a large variety of different projects across biology, medicine and physics promotes links between interdisciplinary research. The development of novel methods and experimental approaches is equally relevant for biosciences and engineering. Data analysis tools that have been, and will be, developed will be shared by all researches. Accordingly, scientists working in any of those areas might be highly interested in the state of the art imaging equipment. The impact will be direct and immediate.

(5) Staff working on the project. Researchers will work interdisciplinary, interact with many scientists of different backgrounds and companies and creatively solve problems. They will further develop communication, problem solving and entrepreneurial skills and acquire new technical and IT skills, which will be useful in any later profession.


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Description The funds were invested in a state-of-the-art microscope which is housed in the imaging core facility of the University; it delivers valuable data for a large number of users.
Exploitation Route contribution to publications
Sectors Education,Healthcare

Description Orchestration of adhesion signalling networks by the tensins and their impact in cell motility and matrix remodelling.
Amount £460,611 (GBP)
Funding ID BB/V016326/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 08/2021 
End 07/2024
Title Mechanical tension system for use on the Upright confocal 
Description Mechanical bi-axial stretching machine that allows cells/eggs/embryos to be imaged while under tension on the upright confocal. The tissue is stuck to the polymer support and attached to the "stretching machine". The control software then allows this support to be accurately and repeatedly "stretched" so that the membrane is held under a constant tension. The system can then be placed on the upright confocal stage and dipping objectives used to image the sample over several hours. This allows the role of tension to be investigated in spindle orientation and control. 
Type Of Material Technology assay or reagent 
Year Produced 2019 
Provided To Others? Yes  
Impact This "stretching machine" allows controlled, accurate and reproducible tension to be applied to cells/tissue/organisms attached to the polymer support. This is a crucial tool in order to investigate the role tension has on normal cell development and provides a method to induce both uni- and bi-directional tension onto these samples while being able to investigate them using high resolution confocal imagining. 
Title Use of micropatterns to examine axon outgrowth and pathfinding 
Description We have established an assay whereby we use light induced micropatterning to study how axon outgrowth and pathfinding is regulated by extracellular matrix components. We recently published the method/assay in JoVE. 
Type Of Material Technology assay or reagent 
Year Produced 2019 
Provided To Others? Yes  
Impact We are teaching this method in Masters courses; it will generate a useful tool for many researchers that are interested how cells respond to specific factors that can be presented in different shapes and concentration gradients. 
Description Collaboration to establish assays of extracellular matrix remodelling. 
Organisation King's College London
Department Randall Division of Cell & Molecular Biophysics
Country United Kingdom 
Sector Academic/University 
PI Contribution Setting up assays that are able to visualise and quantify Matrix remodelling using advanced fluorescence imaging.
Collaborator Contribution Quantitative analysis tools and specific cell lines.
Impact multidisciplinary; collaborations at initial stages.
Start Year 2020
Description Pint of Science 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Public engagement event "Pint of Science" series in Manchester (UK); joint event with an artist (Sally Gilford); Title: Becoming the Matrix.
Year(s) Of Engagement Activity 2022