Visualising infections across scales

Bentley-Abbot, Calum (2026) Visualising infections across scales. PhD thesis, University of Glasgow.

Abstract

The ability to visualise biological structures and processes at the microscale has been instrumental in the development of modern medicine and the control of disease. In recent years, technological innovations have enabled imaging of large, mesoscale tissues, from organs to whole mammalian organisms. However, the development of these methods demonstrates the inherent weaknesses of imaging modalities designed to function at specific length scales. While modern microscale methods enable imaging at resolutions beyond the diffraction limit of light, resolving objects tens of nanometers apart, the field of view and working distance of these systems prevents analysis of mesoscale samples. Conversely, cutting-edge mesoscale imaging methods are capable of imaging whole mice, but lack the resolution of modern confocal microscopes. Holisic analyses are crucial in understanding biological processes and only by designing imaging pipelines capable of coupling high resolution microscopy with large sample mesoscopy can we develop a complete understanding of processes occurring within organisms. Influenza A virus (IAV) exemplifies the need for multiscale imaging approaches. Viral replication is governed by microscale, intracellular processes, while pathology and spread on the scale of the whole lung dictates virus transmission and patient outcomes. Here, I develop methods for imaging tissues across length scales, primarily using IAV as a model pathogen. On the mesoscale, I develop means of visualising infections in whole murine lungs, as well as skin, nerve, and bone tissue without the need for sectioning. On the microscale, I develop computational tools and laboratory assays capable of visualising interactions between viruses, elucidating the processes governing the emergence of viral strains with pandemic potential. By designing holistic imaging pipelines capable of analysing IAV infections across scales, these insights develop a more complete understanding of the spatial context of IAV infection, the interactions between viral populations, and the relationship between microscale processes and meso- and macroscale pathology.

• Item Type: Thesis (PhD)
• Qualification Level: Doctoral
• Subjects: Q Science > QR Microbiology > QR180 Immunology; Q Science > QR Microbiology > QR355 Virology
• Colleges/Schools: College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
• Funder's Name: Wellcome Trust (WELLCOTR)
• Supervisor's Name: Hutchinson, Professor Edward, MacLeod, Professor Annette and Roberts, Dr. Ed
• Date of Award: 2026
• Depositing User: Theses Team
• Unique ID: glathesis:2026-85689
• Copyright: Copyright of this thesis is held by the author.
• Date Deposited: 15 Jan 2026 16:49
• Last Modified: 15 Jan 2026 16:53
• Thesis DOI: 10.5525/gla.thesis.85689
• URI: https://theses.gla.ac.uk/id/eprint/85689

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