Computational Refractive Index Light-sheet Microscopy (CORILIM)
Lead Research Organisation:
UNIVERSITY OF DUNDEE
Department Name: Physics
Abstract
Developing future therapies, the first of EPSRC's Healthcare Technologies Grand Challenges, is essential to keep the National Health Service sustainable. Currently, an estimated 70% of the UK's healthcare expenditure goes towards the management of chronic diseases. Regenerative medicine is expected to significantly reduce costs as it can turn chronic, degenerative, diseases into curable conditions. Realising this potential requires the right tools to study the biological development process as it progresses from the single cell to the complex structure of entire organs.
The invention of the optical microscope, and in particular the phase contrast microscope, made it possible to highlight the fine features of living cells with unprecedented clarity. However, cells isolated on a microscope slide often do not behave as tissue in its natural, three-dimensional, environment. The recent development of the planar illumination light-sheet microscope enabled the visualisation of the intact, fluorescently-labelled, organisms during development. While light-sheet microscopy is highly successful for transparent zebrafish or chemically cleared tissue, many tissues are too opaque to be studied beyond the first layer of cells. A prime example is the chick embryo in its early stages of development. The complex collective behaviour of the cells in the initial layer can be studied in exquisite detail, yet as soon as the primitive streak forms, to grow the embryo in the third dimension, we lack the tools to keep track of the cell migration and differentiation. The images are too blurred.
Correlative refractive index light-sheet microscopy aims to make the invisible visible. It is based on the realization that the turbidity of biological samples is due to the same refractive index variations that yield structural information in phase-contrast microscopy. The distribution of optical properties within the specimen not only contains valuable structural information for the biologist, it also enables the adaptive wavefront correction needed for high resolution fluorescence imaging. By developing a hybrid instrument that maps the optical property distribution in parallel with the fluorescence image, this proposal will enable high-resolution deep-tissue imaging in turbid biological specimen. A direct view into the inner workings of the biological development process is essential to develop effective regenerative-medicine therapies.
The invention of the optical microscope, and in particular the phase contrast microscope, made it possible to highlight the fine features of living cells with unprecedented clarity. However, cells isolated on a microscope slide often do not behave as tissue in its natural, three-dimensional, environment. The recent development of the planar illumination light-sheet microscope enabled the visualisation of the intact, fluorescently-labelled, organisms during development. While light-sheet microscopy is highly successful for transparent zebrafish or chemically cleared tissue, many tissues are too opaque to be studied beyond the first layer of cells. A prime example is the chick embryo in its early stages of development. The complex collective behaviour of the cells in the initial layer can be studied in exquisite detail, yet as soon as the primitive streak forms, to grow the embryo in the third dimension, we lack the tools to keep track of the cell migration and differentiation. The images are too blurred.
Correlative refractive index light-sheet microscopy aims to make the invisible visible. It is based on the realization that the turbidity of biological samples is due to the same refractive index variations that yield structural information in phase-contrast microscopy. The distribution of optical properties within the specimen not only contains valuable structural information for the biologist, it also enables the adaptive wavefront correction needed for high resolution fluorescence imaging. By developing a hybrid instrument that maps the optical property distribution in parallel with the fluorescence image, this proposal will enable high-resolution deep-tissue imaging in turbid biological specimen. A direct view into the inner workings of the biological development process is essential to develop effective regenerative-medicine therapies.
Publications
Beresna M
(2024)
Ultrafast laser processing for optical fibre sensing
Urban D
(2025)
Harmonic OCT for real-time retina flattening
Urban D
(2024)
Advancing Optical Coherence Tomography through Opto-Electronic Frequency Shifting
in EPJ Web of Conferences
Urban DR
(2024)
Widefield optical coherence tomography by electro-optical modulation.
in Biomedical optics express
Valantinas L
(2024)
Scaling Up Wave Calculations with a Scattering Network
in Intelligent Computing
| Description | We developed a method to study the scattering of light waves in complex materials. This is important for the development of the next generation of microscopy technique that allow us to see deeper into biological samples. Such tissue is typically a heterogenous mixture of materials with a range of different optical properties. This scatters the light, thus causing a blur that prevents conventional microscopes from visualising deeper layers. Under certain conditions, adaptive optics and wavefront shaping can undo the scattering, though these methods require precise knowledge of how the waves are scattered. Direct measurements are often impractical and always error prone. On the other hand, solving Maxwell's equations for light used to be a challenge for anything larger than a single biological cell. The computational method that we developed can scale up such calculations by more than two orders of magnitude. My mapping the vector Helmholtz equation onto the structure of the neural network, we were able to leverage tools from machine learning to bring such calculations to a scale relevant in microscopy. With this, we showed that machine learning tools can indeed be used to rigorously solve numeric problems. Neural networks are rapidly transforming our lives by mimicking how humans solve problems. Perhaps unsurprisingly, this carries with it the potential of errors and biases. We showed that a middle ground exists to solve challenging scientific problems with the mathematical rigour expected of scientific computations. Light sheet microscopy can produce sharp 3D images of living tissue. This is great, though when samples are recorded over several hours or even days, the stream of terabytes quickly hits a data processing bottleneck. The problem is exacerbated for more advanced processing techniques such as digital deconvolution. We developed a new algorithm to streamline the data processing pipeline. Typical deconvolution algorithms require the complete 3D data set before processing can start; however, typical sizes are too large to be processed on with GPU hardware acceleration. The new algorithm is able to start the processing as soon as the first few slices of the 3D data set comes in. This means that a typical lab workstation is sufficient to pre-deconvolve light-sheet data on-the-fly. |
| Exploitation Route | 1. The open-source code made available with our paper can immediately be used to solve wave problems in acoustics and electrodynamics. We anticipate that it can also be used to solve more general problems such as diffusion in complex structures, and have published a pre-print to demonstrate how. 2. We will publish the streamlined deconvolution algorithm on open source repositories as soon as the journal paper is published. |
| Sectors | Healthcare |
| Title | Light wave scattering on machine learning infrastructure |
| Description | Computing light scattering in complex materials such as biological tissue is challenging and difficult to scale up. We developed a method to do so more efficiently by leveraging advances in machine learning infrastructure. The method was integrated into the open source electromagnetic solver MacroMax, thereby expanding the functionality of both. The machine-learning enhanced version of MacroMax is freely available, including its complete source code. This enables researchers to scale up their electromagnetic wave calculations, in some cases by more than 2 orders of magnitude. We implemented and distributed this as a Python package, enabling rapid cloud deployment on e.g. Google Colab. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | The computational method is central to the UKRI Future Leaders Fellowship renewal grant award "Computational Refractive Index Light-sheet Microscopy (CORILIM)". We are aware that it is actively used by multiple research groups around the world. The Python package that we developed routinely is routinely downloaded over 400 times per month. |
| URL | https://pypi.org/project/macromax/ |
| Title | Data and code for widefield optical coherence tomography by electro-optical modulation |
| Description | The dataset contains the raw experimental data that support the findings in Urban et al.[1], as well as the Matlab scripts to process it. [1] D. R. Urban et al. "Widefield optical coherence tomography by electro-optical modulation," Biomed. Opt. Express 15 (11), 6573-6587 (2024). https://doi.org/10.1364/BOE.540278 |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | Diseases of the retina often cause blindness and early detection is essential for effective treatment. The first symptoms typically appear in the perifery of the retina, outside the field-of-view of common instruments. The developed technologies improve optical coherence tomography, an important technique for the early detection of eye diseases such as glaucoma, (age-related) macular degeneration, and retinal detachment. These lead to reduced vision and eventually blindness, most certainly a life-altering condition. Early detection is essential to effective treatment. The methods developed and patented are particularly useful to broaden the field-of-view of optical coherence tomography. This can make it possible to study the periphery of the eye, where such diseases tend to develop first. At this stage, our experiments only cover proof-of-principle experiments. Further work is needed to integrate this in existing systems, and later, clinical procedures. The improved imaging capabilities could for instance be used to measure the angle between the iris and the cornea to detect Glaucoma in the anterior segment. Wide area imaging of detect retinal detachment where it first happens. Detection of macular degeneration could potentially benefit from improved signal-to-noise, though this may not be the strongest use case. Eye disease is often first noticed in the periphery. Since the retina and anterior segment are highly curved, any imaging system for the eye must be able to change the imaging depth dynamically during a scan to adapt to the curvature. The developed techniques allow fast (microsecond-scale) electro-optical refocussing of the swept-source OCT system. |
| URL | https://discovery.dundee.ac.uk/en/datasets/data-and-code-for-widefield-optical-coherence-tomography-... |
| Title | Datasets used in Scaling up wave calculations with a Scattering Network |
| Description | The complex-valued field distributions and matrices used to produce the figures in the manuscript "Scaling up wave calculations with a Scattering Network" Intelligent Computing (2024). Data is encoded in Python's NumPy format. Files with the .npy extension store individual complex-valued ndarrays with the field values and permittivity distribution descriptions. Files with the .npz extension store multiple ndarrays to describe the scattering and deposition matrices. The final high resolution / vector graphics versions of the figures are included in Portable Document Format (.pdf). |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | The computational method is central to the UKRI Future Leaders Fellowship renewal grant award "Computational Refractive Index Light-sheet Microscopy (CORILIM)". We are aware that it is actively used by multiple research groups around the world. The Python package that we developed routinely is routinely downloaded over 400 times per month. |
| URL | https://discovery.dundee.ac.uk/en/datasets/datasets-used-in-scaling-up-wave-calculations-with-a-scat... |
| Description | M Squared - bringing novel microscopy techniques to the market |
| Organisation | M Squared Lasers Ltd |
| Department | M Squared Life |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | We lead the development of multiple novel light-sheet illumination techniques in direct collaboration with M Squared lasers. This included the successful concept Planar Airy Light-sheet Microscope. We analysed its performance for single and two-photon microscopy and found that it is ideally suited for two-photon light-sheet microscopy. We rigorously analysed its resolution and field-of-view, and described the novel method in a peer-reviewed manuscript. |
| Collaborator Contribution | M Squared Lasers has been involved from the start of this project and made in-kind contributions. Our many discussions have helped align our research with the market. M Squared has been directly involved in the ideation process to ensure commercial viability. They integrated the planar Airy light-sheet illumination in their commercial Auroraâ„¢ system, evaluated it directly with their development programme customers, and they also contributed to a peer-reviewed publication publication describing the novel technique. |
| Impact | This multi-disciplinary collaboration resulted in the Planar Airy Light-sheet Microscope. It was jointly developed with M Squared Lasers and evaluated by neuroscientists at King's College London. This resulted in a joint peer-reviewed publication that demonstrated the large scale over which brain tissue can be studied with dentritic detail. The technique is now commercially available within M Squared's Auroraâ„¢ microscope system. |
| Start Year | 2020 |
| Description | Nanoscopic retinal functional imaging of neural activity for early disease detection - Optos PLC |
| Organisation | Optos plc |
| Department | Optos |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | The research explores the capability to detect biological nanoscale changes due to retinal neural function, advancing our understanding and diagnostic capabilities in the realm of retinal disease. Optical Coherent Tomography (OCT) serves as a foundational technology for this project. The primary objective is to develop advanced computational methods and stimulus designs to enhance the detection and analysis of retinal neural activity. To achieve this, the research will apply numerical adaptive optics techniques to maximize signal strength and resolution in the targeted retinal layers. A critical component of the methodology involves the design and optimization of spatio-temporal stimulation patterns using a visible light Digital Micro-mirror Device (DMD). These visual patterns will be crafted to achieve maximum excitation of the targeted retinal layers, enabling detection of the associated neural activity. |
| Collaborator Contribution | Our partner, Optos PLC, a Nikon company, contributes both financially (to an EngD student stipend) and in kind (lab space and consumables). Their research team is deeply involved and helps drive the direction of the research. |
| Impact | This is multi-disciplinary, involving optical physics and biomedical. |
| Start Year | 2025 |
| Description | Optos PLC, a Nikon company |
| Organisation | Optos plc |
| Department | Optos |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | This is a quite tight collaboration with weekly meetings and a shared student. My research team and I contribute computational imaging, coherent photonics, and numerical method experience to this project. |
| Collaborator Contribution | Our colleagues at Optos contribute extensive experience in ophalmologic instrument development and application. Much of this work is also done directly at their facility in close collaboration. |
| Impact | Dorian R. Urban, Pavel Novak, Miguel A. Preciado, and Tom Vettenburg "Widefield optical coherence tomography by electro-optical modulation" Biomedical Optics Express Vol. 15, Issue 11, pp. 6573-6587 (2024) https://doi.org/10.1364/BOE.540278 Dorian R. Urban, Pavel Novak, Miguel Preciado and Tom Vettenburg* "Advancing Optical Coherence Tomography through Opto-Electronic Frequency Shifting" EOS Annual Meeting EPJ Web Conf. Volume 309, 2024 https://doi.org/10.1051/epjconf/202430904003 |
| Start Year | 2020 |
| Description | Gravitational Wave Astronomy |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Organized a public talk to encourage pupils to consider physics as a degree. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://bit.ly/PhysCol |
| Description | Hosted EDI event of the Institute of Physics, including a talk on EDI differences between countries. |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | A new Physics Inclusion Award has been put forward by the Institute of Physics. This workshop was to get input from stakeholders from around Scotland. The full-day event included a talk by a colleague who has worked in multiple countries, explaining the differences. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.iop.org/about/IOP-diversity-inclusion/physics-inclusion-award |
| Description | Public talk: Powering Scotland with Renewable Energy |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Organized public talk / discussion about renewable energy with an invited speaker. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://corilim.github.io/outreach/scienceonthetay/ |
| Description | Public talk: The Planeterella & The Aurora |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Organization of a public talk in the Dundee Science Centre to get pupils and their parents excited about physics. |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://bit.ly/PhysCol |