Integrative Biological Imaging Network (IBIN)
Lead Research Organisation:
King's College London
Department Name: Randall Div of Cell and Molecular Biophy
Abstract
To understand and combat the causes of human disease, we must understand the basic structure and function of the individual cells that make up the tissues and organs of the human body. For example, to allow the design of effective therapies to target cancer we first need to answer fundamental questions about how the growth, division and movement of cells are controlled. Robert Hooke was the first to use microscopes to describe cell structure in 1665, and since then microscopy has become one of the most powerful tools for cell biologists across the world. The power of light microscopes has of course continued to increase since their invention but, remarkably, the most dramatic improvement has come in the last ten years or so. In that period physicists have worked out how to measure the location of a single protein in a cell with a precision about ten times better that was previously thought possible. This is important because we can now see the internal structure and organisation of cells in much more detail. In parallel, physicists working together with biologists developed microscopical methods that, instead of just producing a map of the locations of one particular protein inside a cell, can produce a map of precisely where one protein is bound to another. This is a fundamental advance, because cell function is controlled by pathways and networks of such interactions between specific proteins. Potentially these new microscopes provide a window into the internal workings of a cell that allow us to see these protein networks. However, at the moment, the most detailed images can only be obtained from chemically preserved rather than living cells, and each image takes minutes to record. This is a serious problem, because the interactions between proteins that control cell function take place on the time scale of seconds and can occur at different places inside living cells. These methods are also currently restricted to looking at these molecules in single cells, not populations of cells. This provides very limited understanding of how cells communicate within tissues, and how these processes go wrong in different disease settings.
In the present proposal, biologists, physicists, chemists and mathematicians will work together as a team to develop new technology and approaches to image events that occur in live cells within 3-dimensional tissues. By combining ideas from different scientific backgrounds, we will be able to develop novel ways to tackle these problems and train scientists in a range of different types of techniques so they are equipped with key skills to perform innovative new experiments. We think that these new developments will unlock the potential of microscopy to show us how cells work at the molecular level and provide ways for us to analyse how cells work in normal healthy tissues as well as in diseases.
In the present proposal, biologists, physicists, chemists and mathematicians will work together as a team to develop new technology and approaches to image events that occur in live cells within 3-dimensional tissues. By combining ideas from different scientific backgrounds, we will be able to develop novel ways to tackle these problems and train scientists in a range of different types of techniques so they are equipped with key skills to perform innovative new experiments. We think that these new developments will unlock the potential of microscopy to show us how cells work at the molecular level and provide ways for us to analyse how cells work in normal healthy tissues as well as in diseases.
Technical Summary
The ability to image multiple signalling and phenotypic changes across different cell populations in vitro or in vivo, and then integrate and display this information quantitatively, would transform the study of many biological processes. Achieving such imaging and analysis is a major multidisciplinary challenge across the life and physical sciences, which holds the potential to deliver significant impact across a broad range of fundamental and medical fields. The Integrated Biological Imaging Network (IBIN) will combine cell, molecular and in vivo biologists, engineers, physicists, chemists and computational scientists to brainstorm and implement solutions to defining complex tissue-wide biological questions. The combined expertise in microscopy instrument development, cell and in vivo biology, mathematics, chemistry and computer science will provide an excellent framework to develop new strategies to tackle this unmet need. The shared vision is to develop a suite of multi-modal imaging approaches and appropriate biological tools/probes for use in these settings, which will deliver novel biological network information from molecules to mice. Quantitative information on protein dynamics, activation and interactions over this range of length-scales will allow us to understand the short and long term consequences of local signals on cell behaviour, tissue organisation and disease. We will base network discussions and experimental activities around three exemplar biological challenges that encompass the core problems to be tackled, with relevance to both homeostasis and disease mechanisms in the following biological areas: 1) Cell adhesion signalling hierarchy in development and disease; 2) Long-range molecular cues that regulate immune cell behaviour; 3) Tissue mechanics controlling cell growth. IBIN represents an exciting and timely opportunity to harness the broad base of UK expertise to deliver innovative new imaging solutions for complex biological questions.
Planned Impact
We anticipate that IBIN outcomes will provide impact in the following three areas:
Academic:
All network members will benefit directly from the opportunity to talk to people within their discipline who they might not otherwise meet, and across discipline barriers, leading to publications, collaborations and grant applications. Development of the individual techniques and enhanced integration will also benefit the broader scientific community. In addition to the network meetings, we will hold smaller network meet-ups at major conferences. Local network champions will promote the network at local group meetings across the UK. Understanding an order of magnitude change in length-scale and environment is a new frontier, with important biomedical implications.
Industry:
Immediate beneficiaries will be the instrument companies are already involved in the network; they will learn about complex biological questions and the methods that can tackle them, which is an area of considerable developmental interest for industry. We will also engage with other imaging hardware and life sciences companies as the network develops. Thus there are significant direct commercialisation opportunities for software and hardware solutions that emerge from network. Pharmaceutical companies will be key longer-term beneficiaries as the network activities provide broader understanding of the consequences of molecular events at the system level and provide more refined drug discovery approaches. Many of the network members have long-term collaborations with the Pharmaceutical industry and will therefore be very well placed to engage with these stakeholders as the network progresses to identify shared interests and collaboration opportunities.
Dissemination:
Our primary forms of dissemination of network activities will be through shared publications, presentation at external conferences and via our Network organised conference (also open to non-network members) in year 3 of this proposal. We will also ensure local dissemination occurs within Network institutions to identify new potential partners and also to publicise the work we are doing. We will establish a network website to update on network activities and provide means to rapidly feedback useful information to the scientific community and public. Within this we will embed an Online Network forum for virtual conferences and webinars between network members and industrial partners to share ideas and seek advice. If successful we will consider opening this out to non-network members as a core means to promote knowledge exchange. White papers and protocols emerging from the network discussions and activities will be disseminated via publications and made available on-line. We will organise pre-congress sessions at international conferences as well as promotion at exhibitions and networking events. To share our work with the general public, we will set-up 'Microscopy Live' events to encompass live broadcast of talks and demo's via the forum for public engagement. The visualisation of the otherwise invisible world is also an exciting and very appropriate area to engage the public and we will showcase the Network activities through events such as the Royal Society Summer Science Exhibition and 'Pint of Science' events.
Academic:
All network members will benefit directly from the opportunity to talk to people within their discipline who they might not otherwise meet, and across discipline barriers, leading to publications, collaborations and grant applications. Development of the individual techniques and enhanced integration will also benefit the broader scientific community. In addition to the network meetings, we will hold smaller network meet-ups at major conferences. Local network champions will promote the network at local group meetings across the UK. Understanding an order of magnitude change in length-scale and environment is a new frontier, with important biomedical implications.
Industry:
Immediate beneficiaries will be the instrument companies are already involved in the network; they will learn about complex biological questions and the methods that can tackle them, which is an area of considerable developmental interest for industry. We will also engage with other imaging hardware and life sciences companies as the network develops. Thus there are significant direct commercialisation opportunities for software and hardware solutions that emerge from network. Pharmaceutical companies will be key longer-term beneficiaries as the network activities provide broader understanding of the consequences of molecular events at the system level and provide more refined drug discovery approaches. Many of the network members have long-term collaborations with the Pharmaceutical industry and will therefore be very well placed to engage with these stakeholders as the network progresses to identify shared interests and collaboration opportunities.
Dissemination:
Our primary forms of dissemination of network activities will be through shared publications, presentation at external conferences and via our Network organised conference (also open to non-network members) in year 3 of this proposal. We will also ensure local dissemination occurs within Network institutions to identify new potential partners and also to publicise the work we are doing. We will establish a network website to update on network activities and provide means to rapidly feedback useful information to the scientific community and public. Within this we will embed an Online Network forum for virtual conferences and webinars between network members and industrial partners to share ideas and seek advice. If successful we will consider opening this out to non-network members as a core means to promote knowledge exchange. White papers and protocols emerging from the network discussions and activities will be disseminated via publications and made available on-line. We will organise pre-congress sessions at international conferences as well as promotion at exhibitions and networking events. To share our work with the general public, we will set-up 'Microscopy Live' events to encompass live broadcast of talks and demo's via the forum for public engagement. The visualisation of the otherwise invisible world is also an exciting and very appropriate area to engage the public and we will showcase the Network activities through events such as the Royal Society Summer Science Exhibition and 'Pint of Science' events.
Organisations
- King's College London (Lead Research Organisation)
- Engineering and Physical Sciences Research Council (Co-funder)
- Biotechnology and Biological Sciences Research Council (Co-funder)
- Celex Oncology Innovations (Collaboration)
- Leica Microsystems GmbH (Collaboration)
- Leeds Teaching Hospitals NHS Trust (Collaboration)
- National Physical Laboratory (Collaboration)
- Rice University (Collaboration)
- Aix-Marseille University (Collaboration)
- QUEEN MARY UNIVERSITY OF LONDON (Collaboration)
- Hamamatsu Photonics (UK) Ltd (Collaboration)
- Max Planck Society (Collaboration)
- Cellesce Ltd (Collaboration)
- Carl Zeiss AG (Collaboration)
- University of Sheffield (Collaboration)
- Cardiff University (Collaboration)
- Heriot-Watt University (Collaboration)
- UNIVERSITY OF BIRMINGHAM (Collaboration)
- Medicines Discovery Catapult (Collaboration)
- UNIVERSITY OF LEEDS (Collaboration)
- Medical Research Council (MRC) (Collaboration)
- University of Bristol (Collaboration)
- University College London (Collaboration)
- University of Manchester (Collaboration)
- Photometrics UK Ltd (Collaboration)
- UNIVERSITY OF NOTTINGHAM (Collaboration)
- Nikon (Collaboration)
- Newcastle University (Collaboration)
- UNIVERSITY OF STRATHCLYDE (Collaboration)
- Bio-Techne Ltd (Collaboration)
- IMPERIAL COLLEGE LONDON (Collaboration)
- UNIVERSITY OF CAMBRIDGE (Collaboration)
- UNIVERSITY OF OXFORD (Collaboration)
- Swiss Federal Institute of Technology in Lausanne (EPFL) (Collaboration)
- Brown University (Collaboration)
- UNIVERSITY OF GLASGOW (Collaboration)
- University of Huddersfield (Collaboration)
- Abbelight (Collaboration)
- Photon Lines (Collaboration)
- KING'S COLLEGE LONDON (Collaboration)
Publications
Jackson R
(2022)
Correlative Live-Cell and Super-Resolution Imaging to Link Presynaptic Molecular Organisation With Function
in Frontiers in Synaptic Neuroscience
Quicke P
(2021)
Membrane voltage fluctuations in human breast cancer cells
Robbins M
(2021)
Calcium imaging analysis - how far have we come?
in F1000Research
| Title | The Science of Art, the Art of Science |
| Description | The collaborative project is based around a dialogue between the arts and science. The research explores staining cells for immunofluorescence labelling, and process-led sculpture making. The creative process of both participants (Deborah Gardner and Dr Anke Bruning-Ricardson, Biological Sciences, University of Huddersfield) is explored by the viewer by a series of guiding questions. This allows the viewer to engage with the many similarities, thought processes, and methodologies that may not necessarily predict any fixed outcome. Research often uncovers unexpected results as well as art. This workflow is realised by the researcher going through single steps of immunofluorescence leading to microscopic imagery and to a sequential approach of the art practitioner. The whole process is accompanied by lead questions to both artist and scientist whilst working separately on their project, and the whole event has been filmed. The completed movie has already been screened as part of this year's online Otley Science Fair. |
| Type Of Art | Artistic/Creative Exhibition |
| Year Produced | 2020 |
| Impact | Reached the vitual audience of Otley Science Fair. Viewed 27 times on YouTube. 744 impressions on Twitter, with 48 engagements. |
| URL | https://youtube.com/playlist?list=PLhAm9goHdqLQQJHdjssdTiFP7Gb154opO |
| Title | A correlative multicolour imaging approach to link synaptic nanoscale structure with function |
| Description | A pipeline for correlative live-dSTORM imaging of synapses, which is detailed in a forthcoming methods paper. An accompanying Matlab script for registration of the two imaging modalities has been made available at GitHub. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2021 |
| Provided To Others? | No |
| Impact | Jackson*, Compans* & Burrone (2022) Correlative live-cell and super-resolution imaging to link presynaptic molecular organisation with function. Frontiers in Synaptic Neuroscience, in press |
| Title | Developing a Toolbox to Image the Relation between Cells and their Extracellular Matrix |
| Description | The majority of cells and particularly cells named fibroblast synthesise fibrous material, the extracellular matrix, which they deposit and organise in specific patterns in their surrounding. Cells attach to this matrix which is a prerequisite to form functional tissue (i.e. organs). Changes of the biochemical and mechanical properties of the matrix is associated with diseases including cancer, fibrosis and wound healing defects. One of the major gaps in the field is to understand how cells produce and organise this matrix. Here we aimed to develop an experimental pipeline that use the power of high resolution microscopy to image the relation between cells and their extracellular matrix environment. Here is what we have achieved: 1) We have established an imaging pipeline with fibroblasts that were engineered to produce fluorophore coupled collagenI, a fibrous protein that is a critical component for connective tissue and becomes excessively expressed under certain conditions which leads to tissue disfunction (fibrosis). We were able to observe the formation of 3D matrix network which we can now analyse in great detail. 2) We established a live cell imaging protocol where we image cells embedded in this matrix and visualise how they pull on the fibrous material to reorganise it. This required two colour imaging to monitor the fluorescent collagen matrix and the cell cytoskeleton attached to the cell-matrix adhesion machinery. 3) We established a protocol to image the collagen matrix together with another prominent matrix protein named fibronectin. Interestingly, the network of the different types of matrices did overlap only in some areas but not in others. 4) We tested a variety of imaging systems. Some of the somewhat lower resolution (spinning disk) systems performed better in longer term live cell imaging and others (the Airyscan) improved resolution to the cost of live cell imaging capability over longer-term. We experienced also difficulties and it maybe also helpful to mention them for further improvement. It is relatively easy to image exogenously added fluorescent extracellular matrix proteins that then becomes organised by cells or attaches to existing matrix proteins over long periods of time (tested over 24 hours). Settings need to be adjusted to photobleaching. Cells that express fluorescence proteins (as collagenI in our case) are significantly more difficult for imaging since exposure to light causes photodamaging and cellular responses. We are still working on refinement of settings (exposure time, adjustment of culture media, changes in imaging frequency, different type of fluorophores). Overall, all the positive outcomes highlighted above as well as the experience of certain limitations that we aim to overcome in future (by redesigning probes and experimental setups) have put us in a good position to explore in a targeted way the molecular mechanisms of how the cells deposit the matrix. We have submitted further applications that aim to reveal such mechanisms in health and disease. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2021 |
| Provided To Others? | No |
| Impact | The IBIN was excellent to test the boundaries of imaging in 3D. Some of the pioneering experiments did not work out but such pump prime experiments are essential to figure out strength and weaknesses to strengthen a hypothetical approach in project/programme grants. We have established collaborations where we investigate how the synthesis of excess matrix leads to fibrosis and tissue malfunction. We will use experimental pipeline established in this project to shed light into the molecular mechanisms of matrix production and develop further probes to refine our techniques. Submission of grant application to MRC (multimodal research across scales to understand human disease) |
| Title | Development of a long-lifetime dye for gated-STED microscopy |
| Description | This project aimed to develop a new fluorescent dye molecule for use in super-resolution microscopy, specifically for gated-STED microscopy. We have completed the key synthetic steps in the development of our dye design described in the grant proposal. We have also generated cells expressing halotag-tubulin that we will use in our preliminary imaging studies. However, we have not yet had the opportunity to test this dye. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2021 |
| Provided To Others? | No |
| Impact | PhD student Karmjit Grewal continues to work on the development of dyes for super-resolution microscopy. If our dye for gated-STED microscopy proves to be successful, we will build on this by tailoring properties such as improving solubility, targeting and optical properties. This is expected to lead to further research funding applications to e.g. BBSRC or EPSRC. We have been developing new fluorescent dyes for super-resolution microscopy. These dyes have the potential to meet an unmet need for bespoke dyes for state-of-the-art microscopy methods. Through collaborations with biologists and microscopists our dyes will be made available for use in a range of projects and disciplines where access to such tools would be beneficial. We anticipate that the project will lead to the publication of at least one peer-reviewed paper, and potentially more if the dyes are used by other researchers in the future. We will investigate the possibility of protecting IP on dyes developed through this project, while also considering open-access to these tools where possible. |
| Title | Effective labelling of the interior of glioma spheroids with fluorescent nanoparticles. |
| Description | Researchers were able to label the interior of lab-grown brain cancer tumours with fluorescent nanoparticles. They took 3D images of these with high resolution (confocal) and large-volume (light sheet) microscopy. This is useful as part of a route towards improving imaging techniques into 3D biological structures like these tumours, which will lead to improved understanding and treatment of them. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2020 |
| Provided To Others? | No |
| Impact | Not yet. |
| Title | Nonlinear optical microscopy based on transient resonant four-wave-mixing with small gold nanoparticles, providing background free contrast and high spatial resolution in 3D |
| Description | Using an advanced optical microscope built in house in the laboratory of the principal investigator, we have been able to detect and spatially locate in 3D with high image contrast and precision single small gold nanoparticles (NPs) inside the hepatopancreas (HP) of the terrestrial isopod Oniscus asellus (the common woodlouse). This terrestrial isopod can ingest metal NPs from the environment and its HP plays an important role, being involved in metal resistance/tolerance. Notably, due to the wide range of industrial applications with metal NPs, high amounts of them are entering ecosystems, but their fate and effects are still much unknown, and more research should be performed in order to understand their toxicity. With our advanced microscopy technique, we have shown that we can detect gold NPs with high sensitivity (eventually down to a single particle) and precisely locate them inside individual cells in the HP of O. asellus, despite the large size of this organ and its heterogeneity creating an overwhelming scattering background. This work paves the way to an unprecedented understanding of the fate of metallic NPs in these terrestrial isopods as model organisms in soil ecotoxicology. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2021 |
| Provided To Others? | No |
| Impact | The work on the HP of O. asellus has generated first data which we intend to publish in a peer reviewed research article and to use in support of follow-on grant proposals to be funded via NERC or BBSRC. Understanding how metals are transported within organisms can also be applied to medical research (MRC), in relation to metal-related diseases such as Wilson or Menkes disease. The project was supposed to involve correlative electron microscopy with the University of Bristol, but this part of the work proved to be more challenging than anticipated. We intend to continue the collaboration with Bristol to demonstrate a correlative light electron microscopy workflow in the future. |
| Title | Power minimalization through material and computational methods |
| Description | This project is the first study to use BIO133 for the long-term ex vivo culture. This is particularly important for studying the long-term effects of 2-photon stimulation of neurons in living brains after 24 hours, such as for long-term memory assays. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2021 |
| Provided To Others? | No |
| Impact | The aim of the project was for the encapsulation of Drosophila larvae for long-term live animal imaging at reduced power, however the animals were able to move in this material. Therefore, long-term culture of brains for imaging using BIO133 for 2-photon imaging will be used as part of a larger study. In this study, brains are immobilised in BIO133 and neural networks involved in memory formation are stimulated using 2-photon holography. After 24 hours the brains are imaged for changes to GCaMP intensity to look for long-term changes to the plasticity of neural networks. The research will now use the method developed for the immobilisation of larval brains for long-term 2-photon imaging as part of a larger project. This research allowed the collaboration that instigated the review paper, doi: 10.12688/f1000research.51755.2 Further research work |
| Title | Uptake and intracellular trafficking of HER2-targeted multivalent nanoparticles |
| Description | The affibody-apoferritin nanocage platform can be rapidly adapted to target other receptors and also to deliver a range/combination of imaging probes (fluorescent/MRI etc) including quantum dots and other nanoparticles to specific cells. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2021 |
| Provided To Others? | No |
| Impact | In Nottingham, we have generated protein-based nanoparticles decorated with HER2-affibodies on their surface that are capable of carrying a wide range of small molecule drugs (up to 500 drugs per nanoparticle). The IBIN funding has allowed us to initiate a collaboration with Drs Isabel Peset-Martin and Duygu Yilmaz in the microscopy division of the Medicines Discovery Catapult, based at Alderley Park to examine in detail the uptake and fate of these nanoparticles at a single particle level with a variety of HER2-positive breast cancer cell lines and demonstrate very good selectivity for the rate of uptake of these cages in HER2+ cells when compared with cancer cell lines that have normal or low levels of HER2 receptors (as checked by Western blots). The microscopy study involved labelling the nanoparticles with Alexafluor 647 and using labelled HER2-affibodies and trastuzumab (therapeutic anti-HER2 antibody Herceptin) as controls. Using a Opera Phenix Plus HCS confocal spinning disk imaging system (Perkin Elmer), a nuclear stain (DAPI) a cell membrane stain (WGA-Alexa488) and , the binding, uptake and trafficking of the nanoparticles fluorescently labelled could be imaged and quantified. In HER2 positive cancer cells it was found that the nanoparticles were internalized in substantially higher amounts than either the HER2-affibody on its own or trastuzumab whilst in HER-normal/negative cell lines the uptake of the nanocages was significantly less and much closer to that observed with the affibodies on their own or trastuzumab. This validates our hypothesis that the multivalency of the HER2-affibody decorated nanoparticle show significant enhancement in cell uptake. Further image analysis in 2D and 3D demonstrated that the uptake in HER2+ SKBR3 breast cancer cells began to occur after 1 hr and peaked after 4 hrs, with significant amounts of the nanoparticle being observed inside the cells with some close to or at the nuclear membrane after 24 hours. A very preliminary STORM imaging study of the levels of HER2 receptor at the cell membrane or internalized suggested that the affibody decorated nanoparticle internalized and retained significantly more HER2 than trastuzumab |
| Title | Analysis of gastrulation models in vitro using human induced pluripotent stem cells |
| Description | Pipelines have been defined which allowed the analysis of previously acquired data and led to considerations for changes in protocols to allow for better automation of analysis. Specifically, ensuring all compartments within the assay are labelled now allows for easier segmentation. Moreover, anchoring of assembloids will enable to extract true cellular movement. Additionally, alternative staining will allow the segmentation and tracking of individual cells rather than measurements historically done on the population as a whole. Going forward with the alterations to protocols, automation including imaging and on the fly analysis could be fully implemented. |
| Type Of Material | Data analysis technique |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | The appreciation for the data that can be extracted from high content imaging has also identified other parts of the assay which could benefit from imaging analysis, for example defining parameters for organoid growth before the assay takes place. The project has overall given a great training opportunity that will not only be able to be successfully applied to the described project but also integrate into other projects for better imaging and meaningful analysis. We are grateful to IBIN for this opportunity and the results obtained will be leveraged in strengthening our ongoing collaboration and applications. |
| Title | Assembloids: Establishing automated multiparametric imaging of self-assembling Brain Tumour Organoids as a Clinical Decision Support System |
| Description | New microscopic image analysis approaches have been developed tested using bespoke data sets, and as a result, we will now be able to optimize our assembloid methodology in regards with 'real world' application. The outcome is an example of how image analysis considerations can critically inform and aid the optimization of laboratory experiments. |
| Type Of Material | Data analysis technique |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | The project has provided excellent training opportunities for the named researcher and has successfully initiated a collaborative road-map between all project partners working toward the translation of the investigated 3D brain tumour assembloid methodology. |
| Title | Diversity Denoising for Unbiased Intensity Quantification in Fluorescence Microscopy |
| Description | During the project, we investigated how statistics such as the measured intensity of sub-resolution fluorescent emitters can be distorted when denoising is applied. We were able to show analytically (for a simplified case) and by using simulated data how the real distribution of intensities is distorted after denoising. We were able to show that this distortion could be minimized by applying denoising methods that are based on VAEs (variational autoencoders) and are able to account for the uncertainty in their prediction. However, we also found that, when the original intensity distribution is more complex, e.g. multimodal, some degree of distortion remains. Finding methods that handle complex distribution better is a subject for future work. |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2021 |
| Provided To Others? | No |
| Impact | As a first step we will validate the findings our project made on simulated data for real microscopy data. Future work will then include the creation and publication of real and simulated benchmark datasets that will allow us to quantify the distortion of statistics as a result of denoising. This will enable the community to develop and compare a new generation of denoising algorithms that are able to minimise the distortion of image statistics as opposed to simply optimising the signal to noise ratio. During this project we developed software for the realistic simulation of sub-resolution fluorescent objects and further developed our denoising algorithms. So far, the research was presented at the 'Seeing is Believing' conference. We developed several software tools as part of this project. We plan to release them as open source. |
| Title | Extension and validation of a newly developed ImageJ plugin as a 3D analysis and quantification tool of cellular morphologies in 3D microscopy |
| Description | Recent advances in high resolution microscopy and the development of 3D organoids to investigate fundamental biological questions has led to the discovery of striking morphological features not applicable to 2D cell culture systems, such as differential responses to treatment with inhibitors of peripherally located cells versus core location. To assess such variable 3D-phenotypes precisely and accurately an appropriate associated software is urgently required, since 2D analysis of 3D acquired imaging data impairs the accuracy of research findings in biological studies. We had previously developed a novel 3D approach to acquisition, analysis and interpretation of tumour spheroid images. Our research interest in epithelial-to-mesenchymal cell transition and initial findings from mesenchymal-to-amoeboid migratory behaviour led to the development of a workflow incorporating the generation and analysis of 3D data with Instant Structured Illumination Microscopy and a new ImageJ plugin. In this IBIN funded project, we achieved our aims within the 6 months of the project - our novel, created workflow ('Cloudbuster') was able to reconstruct a 3D entity from a range of biological samples including immunohistopathology sections of embedded glioma spheroids and Z-stacks obtained from confocal microscopy. We were able to assess the effect of treatment of spheroids with novel anti-migratory small molecule inhibitors in the form of pointclouds. Low computational effort achieved comparison of basic readout parameters such as distance travelled by single migratory cells, length and number of extending cellular protrusions. We successfully scaled 3000x3000x50 sliced image stacks towards a 1x1x1 ratio, followed by threshold application with subsequent edge detection, transformation to a pointcloud and analysis within five minutes on basic computer systems. |
| Type Of Material | Data analysis technique |
| Year Produced | 2021 |
| Provided To Others? | No |
| Impact | We have already included 'Cloudbuster' (the name of our tool) to recent grant applications. We are looking to include some additional readout parameters and have validated the use of 'Cloudbuster' on Apple Mac computers and PCs. We developed a novel analysis tool. We are currently preparing a manuscript for publication in the next special edition of Interface Focus. |
| Title | Imaging membrane voltage light fields: new views into the pathophysiology of cancer. |
| Description | A two-color ratiometric voltage imaging strategy was developed and applied to image membrane potential in a highly aggressive breast cancer cell line and a non-cancerous breast cancer cell line. A machine-learning pipeline was developed to characterize and classify each cell's membrane potential fluctuations. A subset of the highly cancerous cells exhibited fluctuations in membrane potential, whereas membrane potential in the non-cancerous line was static. Treatment of the non-cancerous line with a growth factor known to stimulate metastasis caused a subset of these cells to exhibit membrane potential fluctuations similar to the metastatic cell line. These results suggest that our membrane potential imaging platform may be able to detect membrane potential fluctuations associated with metastatic processes. Future work will focus on combining this imaging platform with assays for metastatic processes and with optogenetics to reveal the causes and consequences of fluctuating Vm on cancer progression. |
| Type Of Material | Data analysis technique |
| Year Produced | 2021 |
| Provided To Others? | No |
| Impact | Future work will focus on combining this imaging platform with assays for metastatic processes and with optogenetics to reveal the causes and consequences of fluctuating Vm on cancer progression. A two-color ratiometric voltage imaging strategy was developed and applied to image membrane potential in a highly aggressive breast cancer cell line and a non-cancerous breast cancer cell line. A machine-learning feature-based analysis pipeline was developed to characterize and classify each cell's membrane potential fluctuations. Based on this work we have one original research article currently under revision at Communications Biology. It is also on BioRxiv: Membrane voltage fluctuations in human breast cancer cells. Peter Quicke, Yilin Sun, Mar Arias-Garcia, Corey D. Acker, Mustafa B. A. Djamgoz, Chris Bakal, Amanda J. Foust bioRxiv 2021.12.20.473148; doi: https://doi.org/10.1101/2021.12.20.473148 |
| Title | Imaging the spread of herpesvirus infection in organotypical epithelial raft cultures |
| Description | The goal of this project was to establish a long-term, 3D imaging (~24 hours) approach of live virus-infected tissue samples (thickness ~50-100 um) using light sheet microscopy. We have managed to optimise our imaging routine by both adding flexibility to the detection pathway and streamlining the data processing. We were not able to test the imaging routine on the organotypic tissue samples described in the project application since our collaborator had only very restricted access to lab facilities due to the COVID pandemic. Instead, we used 4fold physically expanded virus-infected cells to mimic thick samples. In collaboration with the group of Madeleine Lancaster from the MRC LMB, we have started to establish the generation of brain organoids, a miniaturized and simplified version of the brain, to study herpesvirus infection in our lab. The first custom-built solution to control temperature around our microscope for live imaging was unfortunately not viable. Tested on single cells, heating led to sample drift and inconsistent imaging. We are still in the process of finding a good solution for environmental control. |
| Type Of Material | Data handling & control |
| Year Produced | 2021 |
| Provided To Others? | No |
| Impact | The light sheet microscope in our (diSPIM) was equipped with a 20x detection objective in addition to the already existing 60x objective. The new objective provides a larger field-of-view and has a longer working distance, both necessary for imaging bigger and thicker samples. We have also established a data processing pipeline to automatically split colour channels, denoise images, deskew stacks and deconvolve the volumetric data. Since access in the lab of our collaborator was restricted, we were not able to receive the organotypic tissue samples during our project. In collaboration with Madeleine Lancaster from the MRC LMB, we instead received training in the preparation of brain organoids and started to establish procedures in our lab. The organoids will be used as model tissue for studying herpesvirus infection with an emphasis on the link to neurodegeneration. |
| Title | Supervised deep learning based denoising for subcellular live cell miccrosopy |
| Description | Established a workflow to apply deep learning based image denoising to subcellular imaging of organelle dynamics. This was done using human pluripotent stem cells with endogenous labels for the endoplasmic reticulum and nuclear envelope |
| Type Of Material | Data analysis technique |
| Year Produced | 2020 |
| Provided To Others? | No |
| Impact | This pump-priming award has catalyzed a series of applications on deep learning based segmentation and deonoising for applications in advanced microscopy. |
| Title | software for processing of 2D Mesolens images |
| Description | Researchers evaluated the Mesolens, a giant objective lens that gives high-resolution images over an unusually large field of view, as a tool for imaging healthy and diseased blood specimens. They compared the images to those obtained from standard microscopes. |
| Type Of Material | Data analysis technique |
| Year Produced | 2020 |
| Provided To Others? | No |
| Impact | Not yet! Researchers are still working with the dataset, but in the meantime, they have a paper submitted to Science Advances. |
| Description | 3D super-resolution localisation of virulence factors in intracellular Leishmania parasites. |
| Organisation | Heriot-Watt University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | This multi-disciplinary project brings together expertise in molecular cell biology of parasite-host interactions with advanced super-resolution microscopy, therefore facilitating research which would not be possible at either institution individually. This collaboration will advance the quality of research in this area by not only addressing specific biological questions in parasite-host interactions, but by also benchmarking the dye/fluorophore requirements for effective 3D Tau STED imaging. |
| Impact | Not known. |
| Start Year | 2022 |
| Description | 3D super-resolution localisation of virulence factors in intracellular Leishmania parasites. |
| Organisation | University of Glasgow |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | This multi-disciplinary project brings together expertise in molecular cell biology of parasite-host interactions with advanced super-resolution microscopy, therefore facilitating research which would not be possible at either institution individually. This collaboration will advance the quality of research in this area by not only addressing specific biological questions in parasite-host interactions, but by also benchmarking the dye/fluorophore requirements for effective 3D Tau STED imaging. |
| Impact | Not known. |
| Start Year | 2022 |
| Description | A correlative multicolour imaging approach to link synaptic nanoscale structure with function |
| Organisation | Abbelight |
| Country | France |
| Sector | Private |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | This PDRA-led proposal combines two disciplines, functional imaging at a cellular scale and super-resolution imaging at the nanoscale. Each researcher has expertise in one method; RJ developed sypHy-RGECO, BC has extensive experience in dSTORM and NB will provide the imaging system and technical support from Abbelight. As PDRAs, this award allows us time outside of existing projects to collaborate on combining techniques, exchange knowledge and gain experience in leading independent research. |
| Impact | Not known. |
| Start Year | 2021 |
| Description | A correlative multicolour imaging approach to link synaptic nanoscale structure with function |
| Organisation | King's College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | This PDRA-led proposal combines two disciplines, functional imaging at a cellular scale and super-resolution imaging at the nanoscale. Each researcher has expertise in one method; RJ developed sypHy-RGECO, BC has extensive experience in dSTORM and NB will provide the imaging system and technical support from Abbelight. As PDRAs, this award allows us time outside of existing projects to collaborate on combining techniques, exchange knowledge and gain experience in leading independent research. |
| Impact | Not known. |
| Start Year | 2021 |
| Description | A novel correlative light electron microscopy (CLEM) technique to unravel the nano-toxicology of single gold nanoparticles in terrestrial isopods. |
| Organisation | Cardiff University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | The present project brings together a multidisciplinary team at the physics/life science interface. Prof. Borri (physicist) has invented four-wave-mixing imaging which will be used as the novel LM technique. Dr Ferreira (ECR and Cofund Fellow) and Prof Kille (biologists) are experts in environmental toxicology, molecular biology, and terrestrial isopods. Prof Verkade (biochemist) has a strong internationally-recognised track record in EM, especially in the CLEM workflow. This is a new collaboration which merges cutting-edge technology developments in imaging with relevant biological questions and concerns about NPs in the environment. |
| Impact | Not currently known |
| Start Year | 2019 |
| Description | A novel correlative light electron microscopy (CLEM) technique to unravel the nano-toxicology of single gold nanoparticles in terrestrial isopods. |
| Organisation | University of Bristol |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | The present project brings together a multidisciplinary team at the physics/life science interface. Prof. Borri (physicist) has invented four-wave-mixing imaging which will be used as the novel LM technique. Dr Ferreira (ECR and Cofund Fellow) and Prof Kille (biologists) are experts in environmental toxicology, molecular biology, and terrestrial isopods. Prof Verkade (biochemist) has a strong internationally-recognised track record in EM, especially in the CLEM workflow. This is a new collaboration which merges cutting-edge technology developments in imaging with relevant biological questions and concerns about NPs in the environment. |
| Impact | Not currently known |
| Start Year | 2019 |
| Description | ARHGAP 4, 22 and 25 genes will be silenced or overexpressed in a chosen representative glioma cell line which will then be used for in vivo studies. |
| Organisation | Brown University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | This is a multidisciplinary project combining our expertise in 3D modelling and data acquisition with Dr Lawler's concurrent in vivo models. We will draw on the expertise of Dr Lawler's staff and include other staff at the University of Huddersfield after sabbatical completion. The benefits of this collaboration are multi-layered: It will allow Philippa to experience a novel working environment with the offer of cutting-edge technology and science, enhance her research and her opportunities to publish in high impact factor journals. She will be able to share her newly acquired knowledge at networking events and seminars and enable further collaborations between network members and Dr Lawler's group. It will allow the opportunity to generate data to be highly competitive in the GBM research community. This is an exciting opportunity to establish close collaborative links to a leading Ivy League research institution in the US and the University of Huddersfield and the IBIN network. |
| Impact | Not known. |
| Start Year | 2022 |
| Description | ARHGAP 4, 22 and 25 genes will be silenced or overexpressed in a chosen representative glioma cell line which will then be used for in vivo studies. |
| Organisation | University of Huddersfield |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | This is a multidisciplinary project combining our expertise in 3D modelling and data acquisition with Dr Lawler's concurrent in vivo models. We will draw on the expertise of Dr Lawler's staff and include other staff at the University of Huddersfield after sabbatical completion. The benefits of this collaboration are multi-layered: It will allow Philippa to experience a novel working environment with the offer of cutting-edge technology and science, enhance her research and her opportunities to publish in high impact factor journals. She will be able to share her newly acquired knowledge at networking events and seminars and enable further collaborations between network members and Dr Lawler's group. It will allow the opportunity to generate data to be highly competitive in the GBM research community. This is an exciting opportunity to establish close collaborative links to a leading Ivy League research institution in the US and the University of Huddersfield and the IBIN network. |
| Impact | Not known. |
| Start Year | 2022 |
| Description | Analysis of gastrulation models in vitro using human induced pluripotent stem cells |
| Organisation | King's College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | A nascent collaboration triggered by IBIN; King's, cell lines and initial analysis; NPL, further analysis and single-cell imaging; Gentleman group, gels to embed the cells in Multidisciplinary biological question and methodology combining stem cell biology, materials, high-throughput screening, image and data analysis Deliverables pipelines for spheroid image analysis and screening assays; workflows and infrastructure; future application for funding and translation opportunities |
| Impact | Not currently known. |
| Start Year | 2019 |
| Description | Analysis of gastrulation models in vitro using human induced pluripotent stem cells |
| Organisation | National Physical Laboratory |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | A nascent collaboration triggered by IBIN; King's, cell lines and initial analysis; NPL, further analysis and single-cell imaging; Gentleman group, gels to embed the cells in Multidisciplinary biological question and methodology combining stem cell biology, materials, high-throughput screening, image and data analysis Deliverables pipelines for spheroid image analysis and screening assays; workflows and infrastructure; future application for funding and translation opportunities |
| Impact | Not currently known. |
| Start Year | 2019 |
| Description | Assembloids: Establishing automated multiparametric imaging of self-assembling Brain Tumour Organoids as a Clinical Decision Support System |
| Organisation | Cellesce Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | Is this a multi-disciplinary project? Yes - expertise in patient-derived brain tumour biology modelling (Wurdak, Mathew; Leeds); industrial-scale organoid growth/expansion/characterisation (Duggan/Cellesce; Cardiff); high-throughput 2D/3D phenotyping/glioma-focused chemical/genetic screening (Danovi/Stem Cell Hotel; London). What are the benefits of collaboration? The synergy of these very distinct expertise will maximise the translational value and impact of the 3D brain tumour assembloid methodology. The team covers a broad spectrum of expertise from cell biology to clinics, from imaging to 'scale up' of the methods as diagnostics. |
| Impact | Not currently known. |
| Start Year | 2019 |
| Description | Assembloids: Establishing automated multiparametric imaging of self-assembling Brain Tumour Organoids as a Clinical Decision Support System |
| Organisation | King's College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | Is this a multi-disciplinary project? Yes - expertise in patient-derived brain tumour biology modelling (Wurdak, Mathew; Leeds); industrial-scale organoid growth/expansion/characterisation (Duggan/Cellesce; Cardiff); high-throughput 2D/3D phenotyping/glioma-focused chemical/genetic screening (Danovi/Stem Cell Hotel; London). What are the benefits of collaboration? The synergy of these very distinct expertise will maximise the translational value and impact of the 3D brain tumour assembloid methodology. The team covers a broad spectrum of expertise from cell biology to clinics, from imaging to 'scale up' of the methods as diagnostics. |
| Impact | Not currently known. |
| Start Year | 2019 |
| Description | Assembloids: Establishing automated multiparametric imaging of self-assembling Brain Tumour Organoids as a Clinical Decision Support System |
| Organisation | University of Leeds |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | Is this a multi-disciplinary project? Yes - expertise in patient-derived brain tumour biology modelling (Wurdak, Mathew; Leeds); industrial-scale organoid growth/expansion/characterisation (Duggan/Cellesce; Cardiff); high-throughput 2D/3D phenotyping/glioma-focused chemical/genetic screening (Danovi/Stem Cell Hotel; London). What are the benefits of collaboration? The synergy of these very distinct expertise will maximise the translational value and impact of the 3D brain tumour assembloid methodology. The team covers a broad spectrum of expertise from cell biology to clinics, from imaging to 'scale up' of the methods as diagnostics. |
| Impact | Not currently known. |
| Start Year | 2019 |
| Description | Characterising organelle dynamics and interactions in developing megakaryocytes using 4D microscopy and deep-learning based image restoration. |
| Organisation | Max Planck Society |
| Department | Center for Systems Biology Dresden |
| Country | Germany |
| Sector | Charity/Non Profit |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | This interdisciplinary project requires expertise in MK development (SW, AK), stem cell culture and CRISPR (A.K), advanced microscopy (RH, JP, AK), machine learning (FJ, RH) and image analysis (JP). The new collaborations between the Birmingham Platelet group, COMPARE, and the Henrqiues and Jug groups will bring world leading expertise on applied machine learning and advanced microscopy. This will strengthen IBIN by bringing additional skill sets to the network. |
| Impact | Not known at present |
| Start Year | 2019 |
| Description | Characterising organelle dynamics and interactions in developing megakaryocytes using 4D microscopy and deep-learning based image restoration. |
| Organisation | University College London |
| Department | MRC Laboratory for Molecular Cell Biology |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | This interdisciplinary project requires expertise in MK development (SW, AK), stem cell culture and CRISPR (A.K), advanced microscopy (RH, JP, AK), machine learning (FJ, RH) and image analysis (JP). The new collaborations between the Birmingham Platelet group, COMPARE, and the Henrqiues and Jug groups will bring world leading expertise on applied machine learning and advanced microscopy. This will strengthen IBIN by bringing additional skill sets to the network. |
| Impact | Not known at present |
| Start Year | 2019 |
| Description | Characterising organelle dynamics and interactions in developing megakaryocytes using 4D microscopy and deep-learning based image restoration. |
| Organisation | University of Birmingham |
| Department | School of Biosciences |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | This interdisciplinary project requires expertise in MK development (SW, AK), stem cell culture and CRISPR (A.K), advanced microscopy (RH, JP, AK), machine learning (FJ, RH) and image analysis (JP). The new collaborations between the Birmingham Platelet group, COMPARE, and the Henrqiues and Jug groups will bring world leading expertise on applied machine learning and advanced microscopy. This will strengthen IBIN by bringing additional skill sets to the network. |
| Impact | Not known at present |
| Start Year | 2019 |
| Description | Collaboration and financial contribution from Bio-Techne |
| Organisation | Bio-Techne Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Provided an opportunity in the form of meetings for the industrial partner to have access to researchers. The aim of the collaboration is to create a dialogue between researchers and industry to better guide the research and development programmes of companies to better suit the needs of researchers. |
| Collaborator Contribution | The industrial partner has highlighted potential commercial solutions to 3D Bioimaging challenges. |
| Impact | Ongoing communication between the industrial partner and various researchers. |
| Start Year | 2019 |
| Description | Collaboration and financial contribution from Hamamatsu Photonics UK Ltd |
| Organisation | Hamamatsu Photonics (UK) Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Provided an opportunity in the form of meetings for the industrial partner to have access to researchers. The aim of the collaboration is to create a dialogue between researchers and industry to better guide the research and development programmes of companies to better suit the needs of researchers. |
| Collaborator Contribution | The industrial partner has highlighted potential commercial solutions to 3D Bioimaging challenges. |
| Impact | Ongoing communication between the industrial partner and various researchers. |
| Start Year | 2019 |
| Description | Collaboration and financial contribution from Leica Microsystems (UK) Ltd |
| Organisation | Leica Microsystems GmbH |
| Country | Germany |
| Sector | Private |
| PI Contribution | Provided an opportunity in the form of meetings for the industrial partner to have access to researchers. The aim of the collaboration is to create a dialogue between researchers and industry to better guide the research and development programmes of companies to better suit the needs of researchers. |
| Collaborator Contribution | The industrial partner has highlighted potential commercial solutions to 3D Bioimaging challenges. |
| Impact | Ongoing communication between the industrial partner and various researchers. |
| Start Year | 2019 |
| Description | Collaboration and financial contribution from Nikon |
| Organisation | Nikon |
| Department | Nikon UK |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Provided an opportunity in the form of meetings for the industrial partner to have access to researchers. The aim of the collaboration is to create a dialogue between researchers and industry to better guide the research and development programmes of companies to better suit the needs of researchers. |
| Collaborator Contribution | The industrial partner has highlighted potential commercial solutions to 3D Bioimaging challenges. |
| Impact | Ongoing communication between the industrial partner and various researchers. |
| Start Year | 2019 |
| Description | Collaboration and financial contribution from Photometrics |
| Organisation | Photometrics UK Ltd |
| Country | United States |
| Sector | Private |
| PI Contribution | Provided an opportunity in the form of meetings for the industrial partner to have access to researchers. The aim of the collaboration is to create a dialogue between researchers and industry to better guide the research and development programmes of companies to better suit the needs of researchers. |
| Collaborator Contribution | The industrial partner has highlighted potential commercial solutions to 3D Bioimaging challenges. |
| Impact | Ongoing communication between the industrial partner and various researchers. |
| Start Year | 2019 |
| Description | Collaboration and financial contribution from Photon Lines Uk |
| Organisation | Photon Lines |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Provided an opportunity in the form of meetings for the industrial partner to have access to researchers. The aim of the collaboration is to create a dialogue between researchers and industry to better guide the research and development programmes of companies to better suit the needs of researchers. |
| Collaborator Contribution | The industrial partner has highlighted potential commercial solutions to 3D Bioimaging challenges. |
| Impact | Ongoing communication between the industrial partner and various researchers. |
| Start Year | 2019 |
| Description | Collaboration and financial contribution from Zeiss UK |
| Organisation | Carl Zeiss AG |
| Country | Germany |
| Sector | Private |
| PI Contribution | Provided an opportunity in the form of meetings for the industrial partner to have access to researchers. The aim of the collaboration is to create a dialogue between researchers and industry to better guide the research and development programmes of companies to better suit the needs of researchers. |
| Collaborator Contribution | The industrial partner has highlighted potential commercial solutions to 3D Bioimaging challenges. |
| Impact | Ongoing communication between the industrial partner and various researchers. |
| Start Year | 2019 |
| Description | Deploying hyperspectral camera-based live label-free 4D metabolic imaging |
| Organisation | Imperial College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | This is a multidisciplinary project targeting a very current environmental health problem (deposition of inhaled microplastics in the deep lung), utilising metabolic markers, and longitudinal label-free quantitative imaging (with low phototoxicity) in 3D (X,Y,Z) and 4D (X,Y,Z, t) The group established to deploy hyperspectral imaging is a new collaboration between SA-B and JBS which brings expertise in the fundamental biological question of particle inhalation toxicology (JBS), expertise in advanced microscopy (JBS and SA-B), light sheet and FLIM (SA-B), and in phase and modulation quantitative imaging (JBS and SA-B) |
| Impact | Not known. |
| Start Year | 2022 |
| Description | Deploying hyperspectral camera-based live label-free 4D metabolic imaging |
| Organisation | Imperial College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | This is a multidisciplinary project targeting a very current environmental health problem (deposition of inhaled microplastics in the deep lung), utilising metabolic markers, and longitudinal label-free quantitative imaging (with low phototoxicity) in 3D (X,Y,Z) and 4D (X,Y,Z, t) The group established to deploy hyperspectral imaging is a new collaboration between SA-B and JBS which brings expertise in the fundamental biological question of particle inhalation toxicology (JBS), expertise in advanced microscopy (JBS and SA-B), light sheet and FLIM (SA-B), and in phase and modulation quantitative imaging (JBS and SA-B) |
| Impact | Not known. |
| Start Year | 2022 |
| Description | Deploying hyperspectral camera-based live label-free 4D metabolic imaging |
| Organisation | King's College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | This is a multidisciplinary project targeting a very current environmental health problem (deposition of inhaled microplastics in the deep lung), utilising metabolic markers, and longitudinal label-free quantitative imaging (with low phototoxicity) in 3D (X,Y,Z) and 4D (X,Y,Z, t) The group established to deploy hyperspectral imaging is a new collaboration between SA-B and JBS which brings expertise in the fundamental biological question of particle inhalation toxicology (JBS), expertise in advanced microscopy (JBS and SA-B), light sheet and FLIM (SA-B), and in phase and modulation quantitative imaging (JBS and SA-B) |
| Impact | Not known. |
| Start Year | 2022 |
| Description | Developing a Toolbox to Image the Relation between Cells and their Extracellular Matrix |
| Organisation | King's College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | The collaboration will share resources and expertise to address a big biological problem: • Stramer lab (KCL): access to primary cells (human fibroblasts from normal or keloid skin; CAFs); experience of analysing structural properties of a CDM; collagen labelling and imaging using CNA35 peptide. • Ballestrem lab (Manchester): matrix labelling using fluorophore-conjugated ECM proteins; cell lines expressing fluorophore-linked cytoskeletal and cell adhesion proteins for imaging matrix remodelling. |
| Impact | Not currently known. |
| Start Year | 2020 |
| Description | Developing a Toolbox to Image the Relation between Cells and their Extracellular Matrix |
| Organisation | University of Manchester |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | The collaboration will share resources and expertise to address a big biological problem: • Stramer lab (KCL): access to primary cells (human fibroblasts from normal or keloid skin; CAFs); experience of analysing structural properties of a CDM; collagen labelling and imaging using CNA35 peptide. • Ballestrem lab (Manchester): matrix labelling using fluorophore-conjugated ECM proteins; cell lines expressing fluorophore-linked cytoskeletal and cell adhesion proteins for imaging matrix remodelling. |
| Impact | Not currently known. |
| Start Year | 2020 |
| Description | Developing measurement and analysis tools to correct for optical inhomogeneity in thick samples in high-precision light microscopy. |
| Organisation | University of Birmingham |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | The team consists of microscopy experts AC (physics), ST (cell biology) and DK (microbiology), a cancer spheroid cell biologist (ABR) and a researcher with developing experience in labelling technology and imaging in cell biology (GC). AC processes aberrated 3D PSFs for super-resolution microscopy. ST and DK work with diSPIM (light sheet) for thick 3D samples. The combined expertise in growing spheroids, microscopy techniques, and development of analysis approaches is essential for this project. |
| Impact | Not known at this time |
| Start Year | 2019 |
| Description | Developing measurement and analysis tools to correct for optical inhomogeneity in thick samples in high-precision light microscopy. |
| Organisation | University of Huddersfield |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | The team consists of microscopy experts AC (physics), ST (cell biology) and DK (microbiology), a cancer spheroid cell biologist (ABR) and a researcher with developing experience in labelling technology and imaging in cell biology (GC). AC processes aberrated 3D PSFs for super-resolution microscopy. ST and DK work with diSPIM (light sheet) for thick 3D samples. The combined expertise in growing spheroids, microscopy techniques, and development of analysis approaches is essential for this project. |
| Impact | Not known at this time |
| Start Year | 2019 |
| Description | Developing measurement and analysis tools to correct for optical inhomogeneity in thick samples in high-precision light microscopy. |
| Organisation | University of Leeds |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | The team consists of microscopy experts AC (physics), ST (cell biology) and DK (microbiology), a cancer spheroid cell biologist (ABR) and a researcher with developing experience in labelling technology and imaging in cell biology (GC). AC processes aberrated 3D PSFs for super-resolution microscopy. ST and DK work with diSPIM (light sheet) for thick 3D samples. The combined expertise in growing spheroids, microscopy techniques, and development of analysis approaches is essential for this project. |
| Impact | Not known at this time |
| Start Year | 2019 |
| Description | Developing spatiotemporal analyses of imaging mass cytometry data to investigate therapy-driven changes in cell populations in glioblastoma brain tumours |
| Organisation | Leeds Teaching Hospitals NHS Trust |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | LS (PI) is a computational brain cancer biologist. IM (Co-I) is a consultant neuropathologist at Leeds Teaching Hospitals NHS Trust (LTHT), who has negotiated 2 days/week for academic research if this grant is awarded. EW (Co-I) is an immunologist. SA (named researcher) is a self-funded computational biology PhD student in the Stead lab. This project constitutes a new collaboration between UoL and LTHT to develop novel methods and inspect the value of advanced imaging in clinical practice. |
| Impact | Not known. |
| Start Year | 2021 |
| Description | Developing spatiotemporal analyses of imaging mass cytometry data to investigate therapy-driven changes in cell populations in glioblastoma brain tumours |
| Organisation | University of Leeds |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | LS (PI) is a computational brain cancer biologist. IM (Co-I) is a consultant neuropathologist at Leeds Teaching Hospitals NHS Trust (LTHT), who has negotiated 2 days/week for academic research if this grant is awarded. EW (Co-I) is an immunologist. SA (named researcher) is a self-funded computational biology PhD student in the Stead lab. This project constitutes a new collaboration between UoL and LTHT to develop novel methods and inspect the value of advanced imaging in clinical practice. |
| Impact | Not known. |
| Start Year | 2021 |
| Description | Development of a long-lifetime dye for gated-STED microscopy |
| Organisation | Heriot-Watt University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | This multidisciplinary project brings together a new collaboration of RE (Chemistry), BP (neurobiology) and JV ESRIC). Our collective expertise covers dye synthesis cell biology and sted microscopy as needed for successful and timely project completion. The research will be performed by KG, PhD student with RE. KG is developing related dyes for storm microscopy; this project is complementary. |
| Collaborator Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Impact | Not currently known. |
| Start Year | 2020 |
| Description | Development of a long-lifetime dye for gated-STED microscopy |
| Organisation | University of Strathclyde |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | This multidisciplinary project brings together a new collaboration of RE (Chemistry), BP (neurobiology) and JV ESRIC). Our collective expertise covers dye synthesis cell biology and sted microscopy as needed for successful and timely project completion. The research will be performed by KG, PhD student with RE. KG is developing related dyes for storm microscopy; this project is complementary. |
| Collaborator Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Impact | Not currently known. |
| Start Year | 2020 |
| Description | Diversity Denoising for Unbiased Intensity Quantification in Fluorescence Microscopy |
| Organisation | Max Planck Society |
| Department | Max Planck Institute for Molecular Cell Biology and Genetics |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | The project combines expertise from machine learning, advanced microscopy and software development. AK and FJ are experts in machine learning and denoising, both contributed to DivNoising [4], a central part of the project. FJ and his lab are known for the development of scientific software tools. DC and JP are experts in single molecule microscopy and membrane receptors, which we rely on in our experiments. JP has experience in developing software for single molecule microscopy data. |
| Impact | Not known. |
| Start Year | 2021 |
| Description | Diversity Denoising for Unbiased Intensity Quantification in Fluorescence Microscopy |
| Organisation | University of Birmingham |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | The project combines expertise from machine learning, advanced microscopy and software development. AK and FJ are experts in machine learning and denoising, both contributed to DivNoising [4], a central part of the project. FJ and his lab are known for the development of scientific software tools. DC and JP are experts in single molecule microscopy and membrane receptors, which we rely on in our experiments. JP has experience in developing software for single molecule microscopy data. |
| Impact | Not known. |
| Start Year | 2021 |
| Description | Extension and validation of a newly developed ImageJ plugin as a 3D analysis and quantification tool of cellular morphologies in 3D microscopy |
| Organisation | University of Huddersfield |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | The work relies heavily on a multi-disciplinary collaboration (cancer biology, microscopy, programming) and will strengthen our newly created collaboration for future joint grant applications. ABR is an expert in cancer biology and developed the 3D spheroid invasion assay. AR has expertise in software programming and modelling for scientific research. He developed the named plugin. SK has extensive expertise in cell imaging and microscopy, including live embryo imaging. |
| Impact | Not currently known. |
| Start Year | 2020 |
| Description | Extension and validation of a newly developed ImageJ plugin as a 3D analysis and quantification tool of cellular morphologies in 3D microscopy |
| Organisation | University of Leeds |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | The work relies heavily on a multi-disciplinary collaboration (cancer biology, microscopy, programming) and will strengthen our newly created collaboration for future joint grant applications. ABR is an expert in cancer biology and developed the 3D spheroid invasion assay. AR has expertise in software programming and modelling for scientific research. He developed the named plugin. SK has extensive expertise in cell imaging and microscopy, including live embryo imaging. |
| Impact | Not currently known. |
| Start Year | 2020 |
| Description | High-speed 3D Fluorescence Lifetime Imaging of Force in Cardiomyocytes |
| Organisation | King's College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | The multi-disciplinary team has combined experience in photophysics (SAB), (2 photon) light-sheet microscopy (CM, TK), Fluorescence Lifetime Imaging (SAB, TK), Bessel beams (CM), image processing (KM), optogenetic stimulation via spatial light modulation (CM) and cell biology and electrophysiology (AS, IJ, CM). This project takes existing knowledge of photophysics and novel light sheet imaging in an attempt to understand force and contractility in the context of cardiomyocytes undergoing external modulation. Benefits of Collaboration: New area of research for KCL, development of functional imaging approaches for cardiomyocyte research for Leeds and Glasgow. Application of new functional probe to a novel biological question. Opportunity to acquire preliminary data for a new collaboration which will lead to a responsive mode grant application. |
| Impact | Not currently known. |
| Start Year | 2019 |
| Description | High-speed 3D Fluorescence Lifetime Imaging of Force in Cardiomyocytes |
| Organisation | University of Glasgow |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | The multi-disciplinary team has combined experience in photophysics (SAB), (2 photon) light-sheet microscopy (CM, TK), Fluorescence Lifetime Imaging (SAB, TK), Bessel beams (CM), image processing (KM), optogenetic stimulation via spatial light modulation (CM) and cell biology and electrophysiology (AS, IJ, CM). This project takes existing knowledge of photophysics and novel light sheet imaging in an attempt to understand force and contractility in the context of cardiomyocytes undergoing external modulation. Benefits of Collaboration: New area of research for KCL, development of functional imaging approaches for cardiomyocyte research for Leeds and Glasgow. Application of new functional probe to a novel biological question. Opportunity to acquire preliminary data for a new collaboration which will lead to a responsive mode grant application. |
| Impact | Not currently known. |
| Start Year | 2019 |
| Description | High-speed 3D Fluorescence Lifetime Imaging of Force in Cardiomyocytes |
| Organisation | University of Leeds |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | The multi-disciplinary team has combined experience in photophysics (SAB), (2 photon) light-sheet microscopy (CM, TK), Fluorescence Lifetime Imaging (SAB, TK), Bessel beams (CM), image processing (KM), optogenetic stimulation via spatial light modulation (CM) and cell biology and electrophysiology (AS, IJ, CM). This project takes existing knowledge of photophysics and novel light sheet imaging in an attempt to understand force and contractility in the context of cardiomyocytes undergoing external modulation. Benefits of Collaboration: New area of research for KCL, development of functional imaging approaches for cardiomyocyte research for Leeds and Glasgow. Application of new functional probe to a novel biological question. Opportunity to acquire preliminary data for a new collaboration which will lead to a responsive mode grant application. |
| Impact | Not currently known. |
| Start Year | 2019 |
| Description | Imaging cellular proximity using bioluminescence-induced optogenetics. |
| Organisation | King's College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | This is a new multi-disciplinary collaboration between an imaging biologist (GF) and a biophysical chemist (AJ) with complementary expertise and imaging equipment ideally matching the project requirements. GF and AJ share a common interest in developing new ways to control cellular functions/behaviour. Their labs at KCL and NPL are <1h apart enabling easy travel between sites. Further value is added to the collaboration through academia- industry interaction and the enhancing of KCL-NPL links. |
| Impact | Not currently known. |
| Start Year | 2019 |
| Description | Imaging cellular proximity using bioluminescence-induced optogenetics. |
| Organisation | National Physical Laboratory |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | This is a new multi-disciplinary collaboration between an imaging biologist (GF) and a biophysical chemist (AJ) with complementary expertise and imaging equipment ideally matching the project requirements. GF and AJ share a common interest in developing new ways to control cellular functions/behaviour. Their labs at KCL and NPL are <1h apart enabling easy travel between sites. Further value is added to the collaboration through academia- industry interaction and the enhancing of KCL-NPL links. |
| Impact | Not currently known. |
| Start Year | 2019 |
| Description | Imaging membrane voltage light fields: new views into the pathophysiology of cancer. |
| Organisation | Celex Oncology Innovations |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | We are a new truly multi-disciplinary team comprising the labs of Foust (FL, Bioengineering), Mann (ML, Life Sciences), and Djamgoz (DL, Celex Oncology Innovations) at Imperial. This grant will bring together highly synergistic expertise in light field imaging of functional membrane voltage (FL), with expertise in cancer cell biology (ML) and cancer biophysics (DL). This unique collaboration will improve our understanding of the cancer process and has significant clinical implications. |
| Impact | Not currently known. |
| Start Year | 2020 |
| Description | Imaging membrane voltage light fields: new views into the pathophysiology of cancer. |
| Organisation | Imperial College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | We are a new truly multi-disciplinary team comprising the labs of Foust (FL, Bioengineering), Mann (ML, Life Sciences), and Djamgoz (DL, Celex Oncology Innovations) at Imperial. This grant will bring together highly synergistic expertise in light field imaging of functional membrane voltage (FL), with expertise in cancer cell biology (ML) and cancer biophysics (DL). This unique collaboration will improve our understanding of the cancer process and has significant clinical implications. |
| Impact | Not currently known. |
| Start Year | 2020 |
| Description | Imaging the spread of herpesvirus infection in organotypical epithelial raft cultures |
| Organisation | University of Cambridge |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | The proposed project combines aspects of virology, bioengineering, and fluorescence microscopy. Dr Scherer brings in expertise in herpesvirus imaging and light sheet microscopy. Prof Doorbar studies human papillomavirus (HPV), and his lab makes raft cultures regularly and has established protocols. Prof Kaminski provides imaging facilities in his lab. The collaboration will enable an exchange of knowledge and the collaborators will gain access to technology beneficial for their own research. |
| Impact | Not currently known. |
| Start Year | 2020 |
| Description | Improving illumination and increasing throughput for super-resolution microscopy |
| Organisation | Swiss Federal Institute of Technology in Lausanne (EPFL) |
| Country | Switzerland |
| Sector | Public |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | Is this a multi-disciplinary project? Yes, as it involves Biologists (MP), Physicists (AC, SM) and Biophysicist (DM). Both SM's and MP's lab have implemented iSIM set-ups. What are the benefits of collaboration? MP's group will benefit from SM's and DM's expertise in flat field illumination and high throughput imaging, which will enable her group to improve the iSIM technology at Leeds. MP will additionally bring her expertise in Affimers as a novel tool for super-resolution imaging to SM's group, with this collaboration providing an opportunity to test out selected Affimers for labelling centrioles. |
| Impact | Not Currently Known. |
| Start Year | 2019 |
| Description | Improving illumination and increasing throughput for super-resolution microscopy |
| Organisation | University of Leeds |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | Is this a multi-disciplinary project? Yes, as it involves Biologists (MP), Physicists (AC, SM) and Biophysicist (DM). Both SM's and MP's lab have implemented iSIM set-ups. What are the benefits of collaboration? MP's group will benefit from SM's and DM's expertise in flat field illumination and high throughput imaging, which will enable her group to improve the iSIM technology at Leeds. MP will additionally bring her expertise in Affimers as a novel tool for super-resolution imaging to SM's group, with this collaboration providing an opportunity to test out selected Affimers for labelling centrioles. |
| Impact | Not Currently Known. |
| Start Year | 2019 |
| Description | Interplay between the nanoscale architecture of the axon and its mechanical properties revealed by correlative atomic force and super resolution microscopy |
| Organisation | Aix-Marseille University |
| Country | France |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | Dr I. Mela has advanced the use of correlative atomic force and structured illumination microscopy to characterise changes in the mechanical properties of fibroblasts in response to rearrangements of their actin cytoskeleton. Dr C. Leterrier has extensive expertise in super resolution imaging of neurons and specific elements of their cytoskeletal architecture. The combination of the two fields of expertise will yield substantial new knowledge in the field of neuronal mechanobiology. |
| Impact | Not currently known. |
| Start Year | 2020 |
| Description | Interplay between the nanoscale architecture of the axon and its mechanical properties revealed by correlative atomic force and super resolution microscopy |
| Organisation | University of Cambridge |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | Dr I. Mela has advanced the use of correlative atomic force and structured illumination microscopy to characterise changes in the mechanical properties of fibroblasts in response to rearrangements of their actin cytoskeleton. Dr C. Leterrier has extensive expertise in super resolution imaging of neurons and specific elements of their cytoskeletal architecture. The combination of the two fields of expertise will yield substantial new knowledge in the field of neuronal mechanobiology. |
| Impact | Not currently known. |
| Start Year | 2020 |
| Description | Investigating the role of OPN-CD44 in local invasion of glioblastoma patient-derived stem cell-like cells using high-throughput imaging in biomimetic context |
| Organisation | King's College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | Is this a multi-disciplinary project? Yes. The IBIN pump-prime will facilitate a new collaboration: -Expertise in brain tumour stem cell biology and in vitro modelling, OPN/CD44 microenvironment biology (Coombes, Jason; Inflammation Biology, SIMS, KCL) -High-throughput 2D/3D phenotyping; glioma/stem cells (Danovi, Davide; Tasnag, Victoria/StemCell Hotel; London). What are the benefits of collaboration? Jason Coombes (JDC) is the recipient of a Marie Curie Fellowship to study CD44-OPN relationships in tumour invasion and is in establishment phase as an investigator. This project helps JDC build independence through enabling supportive intellectual collaboration furthering a niche and novel experimental investigative theme. Davide Danovi (DD) has an ongoing nascent programme of GBM stem cell biology and has developed a useful modelling and image analysis pipeline that enables this project, at the 'Stem Cell Hotel' with PhD student Victoria Tsang. This facility is focused on supporting King's projects associated with local collaborative priorities within the school. In doing so, this approach is well-aligned with the research themes associated with the IBIN. |
| Impact | Not known yet. |
| Start Year | 2021 |
| Description | Mapping cell compartment specificity of in situ, NHS-ester linked 'pan' labels in Expansion Microscopy |
| Organisation | University of Leeds |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | Jayasinghe is an early career expert in ExM protocols and optical instrumentation. Suen is an early career cell biologist who has used ExM for imaging C. elegans, so is well suited for bridging these probes towards commonly used model organisms. Sheard is an early career cell biologist who has refined ExM for visualising proteins in single cells. Hence, the interests in method development, applications in whole organisms and single cells are covered well between them. |
| Impact | Not Known |
| Start Year | 2022 |
| Description | Mapping cell compartment specificity of in situ, NHS-ester linked 'pan' labels in Expansion Microscopy |
| Organisation | University of Sheffield |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | Jayasinghe is an early career expert in ExM protocols and optical instrumentation. Suen is an early career cell biologist who has used ExM for imaging C. elegans, so is well suited for bridging these probes towards commonly used model organisms. Sheard is an early career cell biologist who has refined ExM for visualising proteins in single cells. Hence, the interests in method development, applications in whole organisms and single cells are covered well between them. |
| Impact | Not Known |
| Start Year | 2022 |
| Description | Mesoscopic high-throughput, high-resolution screening of blood films for rapid detection of malaria infection |
| Organisation | University of Strathclyde |
| Department | Department of Physics |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | The multi-disciplinary team has combined experience in high throughput bioimaging (GM, MS), optical mesoscopy (GM, RS, LK), image processing (GM, MS, RS, LK), global health and infectious diseases (DFR). This project builds on existing expertise to simplify the imaging pipeline from acquisition to analysis with the overall benefit of reducing the data that must be acquired and analysed to make a diagnosis. |
| Impact | Not currently known. |
| Start Year | 2019 |
| Description | NuetrophilTrack: morphological profiling of neutrophil differentiation using deep learning and live imaging |
| Organisation | University of Oxford |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | This exciting multi-disciplinary project combines expertise from computer vision and genetic screening (Engineering) and molecular immunology (Kennedy) which would create fantastic opportunities for sharing expertise and open avenues to new questions in bioimaging and immunology. HS pioneered the development and application of several image analysis and deep learning approaches for challenging microscopy datasets [2-5]. IU group has successfully established in vitro models for studying immune cell differentiation as well as CRISPR technology for gene deletions. |
| Impact | Not known. |
| Start Year | 2021 |
| Description | Power minimalization through material and computational methods |
| Organisation | Medical Research Council (MRC) |
| Department | MRC Laboratory of Molecular Biology (LMB) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | The project involves neurobiology, bioengineering, and computational methods. The benefits of the collaboration include that both steps 1) and 2) (Lay summary) offer solutions to reduce the power requirements for multiple imaging methods. We will combine both of the techniques proposed in 1) and 2) to demonstrate 2P holographic stimulation and live calcium imaging of, immobilized Drosophila larvae at low power, with denoising based on machine learning methods performed in post-processing. |
| Impact | Not known. |
| Start Year | 2021 |
| Description | Power minimalization through material and computational methods |
| Organisation | University of Cambridge |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | The project involves neurobiology, bioengineering, and computational methods. The benefits of the collaboration include that both steps 1) and 2) (Lay summary) offer solutions to reduce the power requirements for multiple imaging methods. We will combine both of the techniques proposed in 1) and 2) to demonstrate 2P holographic stimulation and live calcium imaging of, immobilized Drosophila larvae at low power, with denoising based on machine learning methods performed in post-processing. |
| Impact | Not known. |
| Start Year | 2021 |
| Description | Set-up of an oblique plane microscope-based screening platform for breast cancer heterogeneity using a multi-gene, multi-colour physio-mimetic 3D model |
| Organisation | Imperial College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | This project will kickstart a new collaboration between cancer research and applied photonics. The amalgamation of disciplines combines expertise on 3D cancer models with a focus on heterogeneity, multi-gene, multi-fluorophore tracing, with an expertise in state-of-the-art microscopy. The benefits will include access to genetically manipulated, traceable samples, imaging of highly complex 3D cultures at highest possible spatial-temporal resolution and the development of a drug screening platform. |
| Impact | Not currently known |
| Start Year | 2019 |
| Description | Spatiotemporal Resolution of Lateral Mobility and Lipid Nanodomain Interactions of the GLP-1 receptor in Pancreatic Beta Cells |
| Organisation | Imperial College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | AT is a molecular cell biologist specialized in beta cell GPCR trafficking/signalling; recently, her studies have been focused on translational pharmacology; JBS is an expert in quantitative fluorescence bioimaging with a special interest in lipid-protein interactions. AO is a PhD student in the AT lab working on the identification of GLP-1R cholesterol binding sites. Together, they form a multidisciplinary team ideally suited to establish the proposed imaging technique in pancreatic beta cells. |
| Impact | Not known |
| Start Year | 2022 |
| Description | The development of DNA-based molecular rulers to measure membrane thickness in live cells |
| Organisation | King's College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | This highly synergistic team have expertise at the forefront of DNA nanotechnology, lipid cell biology and 3D/cancer cell biology. UE and SH have collaborated to catalyse initial ruler development and characterisation. The inclusion of VSM in our multi-disciplinary collaboration allows us to substantially expand the range of our imaging tools, which is essential in understanding how they work and in establishing these tools for use in the broader community. |
| Impact | Not known |
| Start Year | 2022 |
| Description | The development of DNA-based molecular rulers to measure membrane thickness in live cells |
| Organisation | Queen Mary University of London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | This highly synergistic team have expertise at the forefront of DNA nanotechnology, lipid cell biology and 3D/cancer cell biology. UE and SH have collaborated to catalyse initial ruler development and characterisation. The inclusion of VSM in our multi-disciplinary collaboration allows us to substantially expand the range of our imaging tools, which is essential in understanding how they work and in establishing these tools for use in the broader community. |
| Impact | Not known |
| Start Year | 2022 |
| Description | The development of DNA-based molecular rulers to measure membrane thickness in live cells |
| Organisation | University College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | This highly synergistic team have expertise at the forefront of DNA nanotechnology, lipid cell biology and 3D/cancer cell biology. UE and SH have collaborated to catalyse initial ruler development and characterisation. The inclusion of VSM in our multi-disciplinary collaboration allows us to substantially expand the range of our imaging tools, which is essential in understanding how they work and in establishing these tools for use in the broader community. |
| Impact | Not known |
| Start Year | 2022 |
| Description | TopoJunction - Using advanced image analysis to develop a biomimetic topographical 3D substrate for accelerated epithelial barrier formation. |
| Organisation | University of Nottingham |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | This project draws on an interdisciplinary skill set from the University of Nottingham Life Sciences (CET, MV), Centre for Additive Manufacturing (LM) and University of Oxford (HS). Combining biomaterial scientists, engineers and modelling/mathematicians this approach is inherently interdisciplinary would establish a rich hub of mutually beneficial research and opportunities for cross-disciplinary sharing expertise. |
| Impact | Not currently known. |
| Start Year | 2020 |
| Description | TopoJunction - Using advanced image analysis to develop a biomimetic topographical 3D substrate for accelerated epithelial barrier formation. |
| Organisation | University of Oxford |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | This project draws on an interdisciplinary skill set from the University of Nottingham Life Sciences (CET, MV), Centre for Additive Manufacturing (LM) and University of Oxford (HS). Combining biomaterial scientists, engineers and modelling/mathematicians this approach is inherently interdisciplinary would establish a rich hub of mutually beneficial research and opportunities for cross-disciplinary sharing expertise. |
| Impact | Not currently known. |
| Start Year | 2020 |
| Description | Uptake and intracellular trafficking of HER2-targeted multivalent nanoparticles |
| Organisation | Medicines Discovery Catapult |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | Is this a multi-disciplinary project? Yes, it combines Nottingham's expertise to generate new targeted protein-based biologics using protein engineering. with the cellular imaging/tracking expertise of the Medicines Discovery Catapult grp. What are the benefits of collaboration? It will provide a molecular level insight into how the HER2-Afb-Apo NP is taken up by HER2+/- breast cancer cells and how both it and any associated HER2 receptors are trafficked and degraded within the cell. Assist in optimizing the Afb:Apo ratio for maximal HER2 degradation and hence therapeutic effect. |
| Impact | Not currently known. |
| Start Year | 2020 |
| Description | Uptake and intracellular trafficking of HER2-targeted multivalent nanoparticles |
| Organisation | University of Nottingham |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | Is this a multi-disciplinary project? Yes, it combines Nottingham's expertise to generate new targeted protein-based biologics using protein engineering. with the cellular imaging/tracking expertise of the Medicines Discovery Catapult grp. What are the benefits of collaboration? It will provide a molecular level insight into how the HER2-Afb-Apo NP is taken up by HER2+/- breast cancer cells and how both it and any associated HER2 receptors are trafficked and degraded within the cell. Assist in optimizing the Afb:Apo ratio for maximal HER2 degradation and hence therapeutic effect. |
| Impact | Not currently known. |
| Start Year | 2020 |
| Description | collaborate with scientists at the Laboratory for Molecular Biology (LMB) to transfer generalisable 3D reconstruction methods in development at Glasgow University (GU) to a new imaging application. |
| Organisation | Medical Research Council (MRC) |
| Department | MRC Laboratory of Molecular Biology (LMB) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | The proposed sabbatical combines experimental imaging components with computational post- processing. The host researcher (JDM) developed the multi-angle projection imaging system on which this project will be based [1]. DO brings expertise with the relevant computational post-processing, in particular the novel reconstruction algorithms that will be applied to the acquired data, and the Cell Biology Division at LMB will provide biological expertise and support. Collaboration will therefore benefit both parties by facilitating the application of our new method to real-world imaging scenarios while introducing it to the biological community. By collaborating on this project, JDM's imaging platform will be progressed from a 2D projection imaging system to a microscope that offers fast volumetric imaging. We anticipate this will be of significant value to the bio-imaging community, with applications ranging from organelle interactions to calcium signalling and biomechanical readouts. |
| Impact | Not known |
| Start Year | 2022 |
| Description | collaborate with scientists at the Laboratory for Molecular Biology (LMB) to transfer generalisable 3D reconstruction methods in development at Glasgow University (GU) to a new imaging application. |
| Organisation | University of Glasgow |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | The proposed sabbatical combines experimental imaging components with computational post- processing. The host researcher (JDM) developed the multi-angle projection imaging system on which this project will be based [1]. DO brings expertise with the relevant computational post-processing, in particular the novel reconstruction algorithms that will be applied to the acquired data, and the Cell Biology Division at LMB will provide biological expertise and support. Collaboration will therefore benefit both parties by facilitating the application of our new method to real-world imaging scenarios while introducing it to the biological community. By collaborating on this project, JDM's imaging platform will be progressed from a 2D projection imaging system to a microscope that offers fast volumetric imaging. We anticipate this will be of significant value to the bio-imaging community, with applications ranging from organelle interactions to calcium signalling and biomechanical readouts. |
| Impact | Not known |
| Start Year | 2022 |
| Description | design, construct and operate a tilted lightsheet microscope |
| Organisation | Newcastle University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | Not known |
| Impact | Not known |
| Start Year | 2022 |
| Description | design, construct and operate a tilted lightsheet microscope |
| Organisation | Rice University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | IBIN facilitated and funded this collaboration between the above institutions. |
| Collaborator Contribution | Not known |
| Impact | Not known |
| Start Year | 2022 |
| Description | 2nd IBIN meeting |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | 90 Bioimaging researchers and industry representatives gathered to discuss current challenges and solutions related to 3D Bioimaging. Attendees were encouraged to form collaborations and apply for pump-prime funding. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://ibin.org.uk |
| Description | 3rd IBIN meeting |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | A joint two-day meeting co-organised with 3DBioNet, another UKRI network. Up to 145 people signed up to attend with an average of 120 people attending each day. Delegates were encouraged for form collaborations, expand their network and engage with industry and our partner networks. |
| Year(s) Of Engagement Activity | 2020 |
| URL | http://ibin.org.uk |
| Description | Creation of website |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | The website is a central location for all of the information about IBIN. It hosts pages for advertising meetings, workshops, and career opportunities, as well as pages outlining the aims of IBIN and funding available. |
| Year(s) Of Engagement Activity | 2018,2019,2020 |
| URL | http://ibin.org.uk |
| Description | Engagement activities via Twitter |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Using Twitter to build up a following and promote the activities of the Network. Twitter was used for advertising meetings, job opportunities, workshops, and partnerships with industry and other networks. |
| Year(s) Of Engagement Activity | 2018,2019,2020 |
| URL | http://twitter.com/3dbioimaging |
| Description | First IBIN network meeting |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | We held the first annual IBIN workshop, attending by ~100 participants from a wide range of disciplines (biology, chemistry, computational image analysis, physics). The workshop was focused around group discussions and brainstorming ideas to design new collaborations to tackle key emerging challenges in 3D bioimaging. Following the workshop, we have initiated a call for pump-priming, secondment and short term visit proposals to enable the ideas developed to be put into action. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://ibin.org.uk/ |
| Description | Participated in MMC ECR meeting |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Attended ECR meeting to discuss how networks like IBIN can support the development of ECRs |
| Year(s) Of Engagement Activity | 2021 |
| Description | Promoted Network at 3DBioNet Event |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Took part in partner TTL network meeting to promote IBIN activities. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Promoted Network at 3DBioNet Event |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Network Manager attended a meeting for UKRI networ 3DBioNet. Around 50-100 attendees were present and IBIN was discussed and promoted. 3DBioNet members with interests that overlap with IBIN were encouraged to sign up to IBIN. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://ibin.org.uk |
| Description | Ran in-person conference for IBIN network members |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | 80 members of the IBIN network community gathered at the University of Birmingham for an imaging focussed meeting. The meeting consisted of talks from the academics present as well as representatives of industry. The day marked the launch of the fifth pump-prime funding round by IBIN and resulted in the development of novel collaborations between institutions across the UK. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Set up a Slack channel to encourage collaboration |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | To try to encourage further discussion within the bioimaging community we set up a slack channel with multiple threads such as 'career development', 'challenges and solutions', job opportunities. This was to have a centralised searchable space for people to share ideas and ask questions that could be relevant to other members in the community. |
| Year(s) Of Engagement Activity | 2020 |
| URL | http://3dbioimaging.slack.com |
| Description | Supported a public engagement activity |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Provided funds for a collaboration between a researcher and artist as part of a project for a public-facing science fair. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://youtube.com/playlist?list=PLhAm9goHdqLQQJHdjssdTiFP7Gb154opO |
| Description | Table-top Microscopy Demo |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | IBIN member paricipated in table top activities and demonstrations on microscopy, imaging and optics at the Explorathon aka European Researchers' Night, the Glasgow Science Festival, the Girls into Physics initiative, the School of Physics and Astronomy Bring your children to work day and Cell Block Science for learners in HMP Shotts. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Technology Touch Life cross network virtual meeting |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | The five UKRI funded TTL networks - 3DBioNet, Imaging BioPro, Integrated Biological Imaging, Organ-on-a-Chip Technologies & PhenomUK - are jointly organising this two day event to show achievements made over the past three years and discuss future directions for the networks. By facilitating partnerships between engineers, physical sciences researchers and health and life scientists - the networks' purpose is to nurture the adventurous research needed to develop the next generation of advanced technology. Together the five networks have over 1000 members and the reach of this event was significant. The meeting was used as an opportunity to gather feedback from members on how the networks have been operating and how they would prefer to see future networks developed. The feedback was passed on to UKRI to influence their future strategies. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Took part in Imaging Facilities Coffee Morning |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Informal discussions with Facilities Managers to promote IBIN and discuss mutual benefits. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Virtual IBIN Member Conference |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Virtual two-day conference over Zoom with members of the IBIN network. The aim was to promote collaboration and networking amongst members as well as launch the next IBIN funding round. The conference consisted of a two-hour session of talks and a two-hour session of informal discussions. |
| Year(s) Of Engagement Activity | 2020 |