Live 3D Confocal Imaging in real time with high throughput, multipoint, targeted acquisition and AI-assisted quantification

Lead Research Organisation: University of Nottingham
Department Name: School of Life Sciences


Imaging is a powerful tool used to understand and exploit the fundamental processes within cells and tissues. Since the microscope was discovered in the late 1500s, there have been many technical advances in the magnification and sensitivity it can achieve. It is now possible to track single molecules in real time within cells as small as bacteria using super resolution microscopy. It is also possible to take a series of vertical images (optical slices) to build up a precise 3D reconstruction of tissue samples and microbes. If this is performed using confocal microscopy there is minimal background light from adjacent slices making the resolution and sensitivity of the final images precise. These advances are facilitating the elucidation of interactions between molecules (e.g. an antimicrobial with its target), interactions between host cells and invading microbes, processes within tumours and also the engineering of bacteria/fungi to generate products of use to us (e.g. biofuels).

Currently there is a bottleneck in the screening of (i) cells to identify which we can exploit, or (ii) novel compounds that we could develop into effective drugs. The delay is caused because the highest resolution microscopes only view one sample at a time. Developers are now building high resolution microscopes that process multiple samples automatically, enabling high throughput screening. We are requesting support to purchase one of the newest generation of microscopes: a high throughput, high content imaging system (HCS).

Recently step change improvements in HCS have brought to the market HCS with confocal and super resolution capabilities that are guided by machine learning. The power of artificial intelligence (AI)-driven image acquisition is that the HCS can scan multiple samples at low resolution and be trained to focus in on interesting areas for high resolution imaging. In this way, the speed of the screening is increased and the automation reduces error.

Two additional features of this new generation of microscopes are particularly relevant for the research we propose to undertake. Firstly, the confocal HCS has a sterilizable sample holder. We will exploit this by installing the HCS in a laboratory with the safety containment required for the study of infectious microbes. Secondly, the equipment includes a cabinet in which we can control the environment. This will enable us to provide the best conditions for maintaining the system under study e.g. low or high oxygen/humidity/optimal temperature (e.g. different microbes and 3D tissue models) and allow us to follow cellular process by undertaking time-lapse imaging at high resolution.

Equipment with the high specification requested will be the first such facility in the Midlands. Our application has the support of the Midlands Innovation network of Universities as well as considerable support from industry partners. Notably, the National Biofilm Innovation Centre is supporting our application because the 31 universities and >60 companies that it partners with would be able to exploit the HCS in their biofilm research. We predict that a confocal HCS will make a real difference to the pipeline of new medicines (antibiotic, anti-viral, anti-biofilm, fungicides, anti-tumour) and exploitable products generated using microbes. These advances will improve the health and wealth of the nation.

The HCS will be managed by an experienced imaging team (SLIM) with a track record in maintaining and supporting the use of a portfolio of microscopes by internal and external scientists. SLIM will expand its thorough training programme to ensure users are fully skilled in HCS handling, and thereby support their career development and maximise the potential of the output from the HCS. The availability of the HCS will be publicised through equipment catalogues and web pages to the research community and industry. The images created will be integrated into ongoing outreach activities.

Technical Summary

The new generation High content imaging systems (HCS) recently released to the market deliver step change improvements including confocal and super resolution image acquisition that is AI-driven. Together, state-of-the-art optics and software provide quantified, high resolution 3D imaging with enhanced sensitivity and precision that do not compromise speed. The flexibility to image slides, multi-well plates and complex 3D tissue models coupled with a chamber providing environmental conditions eg. temperature (5 to 44oC), anaerobic, humidity, will support live cell imaging in physiologically relevant conditions over time. Sterilizable sample holders facilitate the study of live pathogens and we will house the equipment in a Biological safely level 2 environment. Fundamental pathogen research is restricted by lack of access to equipment for screening chemical and microbial libraries. We are limited to low throughput, single point confocal analysis without quantification. The confocal HCS requested will overcome these current hurdles to enable multipoint, rapid quantification of live cells in 3D over time. High throughput, high resolution screens will support translational research (novel antimicrobial/anti-tumour agents and engineered microbes generating useful products e.g. biofuels), as well as supporting phenotypic screens and mechanistic evaluations.

We will create the first such facility in the Midlands and provide broad access via the National Biofilm Innovation Centre (NBIC) and Midlands Innovation Group. Two systems on the market meet our needs: Zeiss Cell discoverer 7-LSM 900 and Nikon LIPSI. Both have >5 objective settings spanning 5-100x, filters and LED light sources to detect a broad range of fluorescence markers. The HCS will be managed by the well-established SLIM team that will provide expert user training and access across the University and externally.


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Description The most significant achievement from this award was the installation and commissioning of a cutting edge, high throughput, high content imaging system in Biological safety level 2 laboratories at the University of Nottingham. This was installed downstream of a liquid handling robot and connected to high speed cloud storage to ensure appropriate data management. In so doing, this fully satisfied Objective 1.
Exploitation Route The current investigator team are still in place, and poised to take forward these objectives towards tangible outcomes in the form of collaborations, funding and publications.
Sectors Healthcare,Pharmaceuticals and Medical Biotechnology

Description Since the high content imaging system has only been installed for a handful of months, the impact is limited. However the attractiveness of the cutting edge facility is already attracting interest and investment from industry, and the high throughput aspect is speeding the data generation of applied and fundamental research projects. The researchers and companies clearly see the potential, and are starting to formulate more ambitious projects in new research areas. This offers the opportunity for step change in pathogen detection and treatment strategies.
First Year Of Impact 2023
Sector Healthcare
Impact Types Societal

Description 20ALERT Live 3D Confocal Imaging in real time with high throughput, multipoint, targeted acquisition and AI-assisted quantification
Amount £700,000 (GBP)
Funding ID BB/V019414/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 11/2021 
End 11/2022
Description Joint Research Studentship Project University of Nottingham and the University of Tübingen Role of the stringent response to promote biocide induced antibiotic tolerance in Staphylococcus aureus biofilms.
Amount £150,000 (GBP)
Organisation University of Nottingham 
Sector Academic/University
Country United Kingdom
Start 09/2022 
End 09/2025
Description Anti biofilm lactam technology 
Organisation Unilever
Country United Kingdom 
Sector Private 
PI Contribution prior knowledge on biofilm and anti-biofilm protocols and related microbiology. chemical synthesis and bacterial strains.
Collaborator Contribution discussion of project processes, provision of reagents, industrial placement
Impact not yet
Start Year 2019
Description National Biofilm and Innovation Centre 
Organisation National Biofilms Innovation Centre
Sector Private 
PI Contribution The academic and industrial partners of NBIC are writing grants to use the high throughput confocal imaging platform set up through this ALERT bid. The researcher fellows of NBIC have been trained in its use and are already generating improved data with it.
Collaborator Contribution NBIC is fostering links for joint grant applications, and underpinning the set up of joint projects funded by industry to use the high content confocal
Impact It is too early to have outcomes as the microscope has only just been commissioned for use, and there is still some work up for risk assessments and protocol development. Plus a couple of components are still required (e.g. multipoint software extension) that have been identified in this initial set up
Start Year 2023
Description Smith & Nephew 
Organisation Smith and Nephew
Department Smith and Nephew Wound Management
Country United Kingdom 
Sector Private 
PI Contribution A researcher from our team will be undertaking a services rendered proof of concept project on the high content imaging platform. Bacterial strains will also be provided, and the expertise in imaging.
Collaborator Contribution S&N will provide wound dressings for analysis and previous experience in the analysis
Impact Only just about to start, so too early for output.
Start Year 2023
Description Visualising pH in oral biofilms 
Organisation Unilever
Country United Kingdom 
Sector Private 
PI Contribution We are contributing know how which includes a biofilm model incorporating Steptococcus mutans and also pH sensitive optical nanosensors
Collaborator Contribution Unilever are financing a post doctoral researcher to undertake the research, plus the know how behind the active ingredients in their products to test
Impact One manuscript submitted and available on a preprint server. Yes, it is multi-disciplinary since it incorporates microbiology to investigate the bacteria, chemistry to build the nanosensors and physics to optimise the imaging. Blunk, B., Perkins, M., Chauhan, V.M, Aylott, J.W., and Hardie, K.R. (2020) Fluorescent Nanosensors Reveal Dynamic pH Gradients During Biofilm Formation.
Start Year 2021
Description NBIC-Medlink Workshop 2023 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact The Event aim is to showcase NBIC to the Midlands as part of the levelling up agenda. Talks provide an overview of the updated Pathogen Imaging Centre by the School of Life Sciences Imaging (SLIM) experts along with tours that provide an outline of the capabilities of the state of the art High Content Imaging System installed through ALERT funding. Other talks covered successful translational projects and pitches from the academic and industrial delegates.
Year(s) Of Engagement Activity 2023