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Mi Qi Lim - Yuriy CBIAS_2023_poster_18_SK_MQ.pdf (1.29 MB)

Development of cluster analysis tools for high throughput single molecule localisation microscopy

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posted on 2023-11-30, 13:09 authored by Mi Qi Lim, Yuriy AlexandrovYuriy Alexandrov, Edwin Garcia, Sean Baccas, Jonathan LightleyJonathan Lightley, Sunil KumarSunil Kumar, Christopher DunsbyChristopher Dunsby, Ian McNeish, Mark NeilMark Neil, Andrew Rose, Paul FrenchPaul French

Poster presented as part of the Crick BioImage Analysis Symposium 2023.

With single molecule localisation microscopy (SMLM), biological nanoarchitecture can be interrogated to explore cell physiology. We aim to widen access to SMLM by developing cost-effective open-source instruments with capability for high throughput SMLM. Aiming to assay changes in ultrastructure, we apply cluster analysis and are working to address the challenges of quantifying densely packed, diverse and complex spatial features that may be present. Current SMLM cluster analysis approaches have some drawbacks:

  • Conventional distance-based algorithms (e.g., triangulation and DBSCAN) are intrinsically slow, requiring so much computer memory that is impractical to analyse more than one nucleus at a time
  • Most cluster analysis methods critically depend on user tuning of multiple parameters
  • Most cluster analysis methods are challenged by structures expressed at multiple scales, and/or that overlap
  • All cluster analysis methods are sensitive to instrumentation-related artefacts

We are working to alleviate these issues while applying SMLM cluster analysis to study changes in chromatin ultrastructure, including to probe mechanisms of resistance to platinum-based chemotherapy.


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