Please see below descriptions of all projects involving Simon Schultz

Simon Schultz Graph theoretic analysis of memory encoding and recall, with applications to dementia Desk based Computational and theoretical modelling, Neurotechnology and robotics

In this project you will apply graph or network theory to neural population recordings obtained by two-photon imaging in a mouse performing memory encoding and recall tasks. The aim is to determine how old information is reorganised when the mouse learns new information. Some of our data is collected from the 5xFAD mouse model of Alzheimer's Disease, and one aim of the project will be to assess how this process is disrupted due to amyloid pathology. There is scope for multiple students to work within this project, carrying out distinct analyses of the dataset.


Simon Schultz, Mary Ann Go

Imaging at cellular resolution deep into living tissue using three-photon microscopy

Lab based

Biomedical sensing diagnostics and imaging, Neurotechnology and robotics

The Department was recently awarded a Wellcome Trust Equipment Award to set up a Three-Photon Microscope (3PM) Facility - the equipment is now in place (one of only a few such installations in Europe). Three-photon microscopy allows us to perform very deep imaging of living tissue - in principle up to several millimetres deep, depending on the optical properties of the tissue imaged, and the fluorescent label used. In this project we will explore the limits of 3PM, and perform a number of proof-of-principle experiments demonstrating imaging through thick biological specimens. This will include imaging structure in fixed tissue samples, imaging the full depth of stem cell organoid cultures, imaging cerebral blood vessels labelled by i.v. injection of dextrans, and imaging neurons in deep tissue labelled by viral injection of fluorescent proteins and genetically encoded calcium indicators. The project will involve biomedical optics laboratory work, wet lab work for preparation of tissue samples, and (in collaboration) in vivo work.

Simon Schultz

Mapping amyloid plaques in whole brains using serial section two photon tomography

Lab based

Neurotechnology and robotics

Alzheimer’s Disease (AD) is the most common type of dementia – accounting for about 70% of the nearly 50 million dementia cases in the world. It is characterised by neuronal degeneration caused by the presence of extracellular amyloid plaques and neurofibrillary tangles in the brain. Genetically modified rodent models have helped advance our understanding of the underlying mechanisms of this disease. One of these models, called 5xFAD, recapitulates many AD-related phenotypes and has a relatively early and aggressive presentation. Amyloid plaques are seen in mice as young as two months of age. However, the degree to which the amyloid plaques affect behavioural performance in these models is still not well known. In this study, high throughput serial two-photon whole brain imaging will be performed in order to map the spatial distribution of amyloid plaques across age in 5xFAD mice, labelled with Methoxy-X04, using the TissueCyte imaging platform. Together with the region-specific progression of plaque densities in critically affected brain structures, these models present an invaluable tool for early intervention and improved pre-clinical assessment of potential therapeutic approaches for AD. This project will involve wet lab work as well as development of python or MATLAB based image analysis code.

Simon Schultz

Tracking changes in brain organoid spontaneous activity over maturation

Lab based

Biomedical sensing diagnostics and imaging,Neurotechnology and robotics

The recent development of 3D cell culture methods for producing cerebral organoids may lead to patient-specific models of neurodevelopmental and neurodegenerative diseases derived from induced pluripotent stem cells from the patient themselves. However, such models differ from in vivo models in that only spontaneous neural dynamics can be observed, rather than the dynamics of neural activity while an animal is performing a relevant task. In this project we will track neural activity from many hundreds of cells over months as human brain organoids develop. We will apply algorithms based on graph heory and information theory for analysing the dynamics, and observing changes. We will then compare the dynamics over developmental age, and potentially compare human brain organoids with those made from other species, such as mice.
This project will involve training in tissue culture, multiphoton imaging, and neural data analysis using python.

Lancaster, M.A., Renner, M., Martin, C.A., Wenzel, D., Bicknell, L.S., Hurles, M.E., Homfray, T., Penninger, J.M., Jackson, A.P. and Knoblich, J.A., 2013. Cerebral organoids model human brain development and microcephaly. Nature, 501(7467), pp.373-379.
Lancaster, M.A. and Knoblich, J.A., 2014. Organogenesis in a dish: modeling development and disease using organoid technologies. Science, 345(6194).
Giandomenico, S.L., Sutcliffe, M. and Lancaster, M.A., 2021. Generation and long-term culture of advanced cerebral organoids for studying later stages of neural development. Nature Protocols, 16(2), pp.579-602.
Gava, G.P., McHugh, S.B., Lefèvre, L., Lopes-dos-Santos, V., Trouche, S., El-Gaby, M., Schultz, S.R. and Dupret, D., 2021. Integrating new memories into the hippocampal network activity space. Nature neuroscience, 24(3), pp.326-330.

Simon Schultz

Three-photon imaging deep into biological tissue

Lab based

Biomedical sensing diagnostics & imaging

Fluorescence microscopy has over the past few decades transformed the biological sciences. By selectively labelling individual cell types with fluorescent tags or reporters, it has been possible to use light microscopes to watch structural and functional changes in tissue in real time. Unfortunately, standard "single photon" fluorescence can only be imaged from superficial tissue (~100 microns) at optical wavelengths, due to scattering. Two-photon excitation fluorescence imaging can be achieved down to ~500 microns in many biological tissues, however this is still not enough to see many biological processes. Three-photon excitation (requiring a high energy laser producing 50 femtosecond pulses) allows us to image around 2 millimetres through intact, functioning tissue. We are lucky here at Imperial College to have one of the few three-photon microscopes in Europe. This project will involve working closely with the facility manager, Dr Mary Ann Go, to explore the limits of three-photon imaging of  variety of tissues, including brain, heart and lung (the latter in collaboration with the National Heart and Lung Institute). The project student will receive training in biomedical optics, microscopy of living tissue, and biomedical image analysis. The end product of the project will be a gallery of three-photon images and movies acquired from deep within living tissue, as well as a publication in an optical microscopy journal.

Darryl Overby & Simon Schultz

Brain-on-Chip: A Novel Explant Perfusion Model for ex vivo Study of Brain Tissue Function

Lab based Biomechanics & mechanobiology; Biomedical sensing diagnostics & imaging; 

The neuroscience community aims to study neural and glial cells in their native microenvironment. Typically, this requires intravital techniques, such as implantation of intracranial windows, or advanced 3D models such as organoids. In this project, we aim to develop a device to preserve the viability and function of murine brain explants for ex vivo analysis of neural function, building on a successful design already applied to liver explants.

This is a multi-disciplinary project that combines the organ-on-chip expertise of the Overby lab with the vital imaging and neuroscience expertise of the Schultz lab.

The existing device works by placing an explant within a semi-conical microchannel constriction. When a pressure drop is applied across the explant, the constriction achieves “self-sealing” between the explant and channel wall, such that flow is forced to pass through (rather than around) the explant. Our data show that perfusion preserves explant viability and function for up to 6 days in murine liver explants.

This project will interface with a team of researchers to adapt the current explant-in-chip design to murine brain. We aim to measure viability markers as a function of perfusion time, assess flow through the microvasculature, and measure neural cell function using voltage-sensitive dyes.

A good student will have enthusiasm for multi-disciplinary science, microfabrication and a willingness to learn and develop new experimental techniques.