A5019498945- Advanced Fluorescence Microscopy Techniques
- Cell Image Analysis Techniques
- Single-cell and spatial transcriptomics
- Advanced Electron Microscopy Techniques and Applications
- Advanced Biosensing Techniques and Applications
- Image Processing Techniques and Applications
- Cell Adhesion Molecules Research
- Lipid Membrane Structure and Behavior
- T-cell and B-cell Immunology
- Cellular transport and secretion
- AI in cancer detection
- Immunotherapy and Immune Responses
- Photosynthetic Processes and Mechanisms
- Protein Tyrosine Phosphatases
- Advanced Nanomaterials in Catalysis
- Digital Holography and Microscopy
- Industrial Vision Systems and Defect Detection
- Optical Coherence Tomography Applications
- Immune Response and Inflammation
- Neuroinflammation and Neurodegeneration Mechanisms
- Galectins and Cancer Biology
- Optical measurement and interference techniques
- Bacteriophages and microbial interactions
- Advanced biosensing and bioanalysis techniques
- Cellular Mechanics and Interactions
Stockholm University
2023-2025
École Polytechnique Fédérale de Lausanne
2019-2024
Science for Life Laboratory
2024
King's College London
2015-2020
King's College School
2017
Single-molecule localization microscopy (SMLM) describes a family of powerful imaging techniques that dramatically improve spatial resolution over standard, diffraction-limited and can image biological structures at the molecular scale. In SMLM, individual fluorescent molecules are computationally localized from sequences localizations used to generate super-resolution or time course images, define trajectories. this Primer, we introduce basic principles SMLM before describing main...
Abstract Quantifying the extent to which points are clustered in single-molecule localization microscopy data is vital understanding spatial relationships between molecules underlying sample. Many existing computational approaches limited their ability process large-scale sets, deal effectively with sample heterogeneity, or require subjective user-defined analysis parameters. Here, we develop a supervised machine-learning approach cluster fast and accurate. Trained on variety of simulated...
Single-molecule localisation microscopy (SMLM) allows the of fluorophores with a precision 10-30 nm, revealing cell's nanoscale architecture at molecular level. Recently, SMLM has been extended to 3D, providing unique insight into cellular machinery. Although cluster analysis techniques have developed for 2D data sets, few applied 3D. This lack quantification tools can be explained by relative novelty imaging such as interferometric photo-activated (iPALM). Also, existing methods that could...
Integrins are heterodimeric transmembrane proteins that play a fundamental role in the migration of leukocytes to sites infection or injury. We found protein tyrosine phosphatase nonreceptor type 22 (PTPN22) inhibits signaling by integrin lymphocyte function-associated antigen-1 (LFA-1) effector T cells. PTPN22 colocalized with its substrates at leading edge cells migrating on surfaces coated LFA-1 ligand intercellular adhesion molecule-1 (ICAM-1). Knockout knockdown expression autoimmune...
A key function of the plasma membrane is regulating signal transduction. Proteins involved in transduction process play a signal-processing role; mapping an input (e.g. number engaged receptors) to output level downstream phosphorylation). In many cases, digital desirable, i.e. that cell activates or responds fully once set threshold surpassed. It believed nanoscale organisation proteins, such as their clustering, modulates this behaviour by altering frequency protein-protein interactions....
Live-cell imaging provides a unique insight into complex cellular processes including single cell fate, but remains limited by both low-throughput and the lack of generalisable analytics for multidimensional datasets it produces. This work introduces AI4CellFate, an interpretable data-driven machine learning framework predicting fate from microscopy timelapses, applied here to cancer therapy. By integrating generative AI contrastive learning, AI4CellFate enables early prediction as well...
Single‐molecule localisation based super‐resolution fluorescence imaging produces maps of the coordinates fluorescent molecules in a region interest. Cluster analysis algorithms provide information concerning clustering characteristics these molecules, often through generation cluster heat on local molecular density. The goal this study was to generate new method topographic approach. In particular, map level across is generated Getis' variant Ripley's K ‐function. By using relative heights...
Abstract Single molecule localization microscopy (SMLM) methods produce data in the form of a spatial point pattern (SPP) all localized emitters. Whilst numerous tools exist to quantify molecular clustering SPP data, analysis fibrous structures has remained understudied. Taking SMLM coordinates as input, we present an algorithm capable tracing generated by SMLM. Based upon density parameter routine, outputs several fibre descriptors, such number fibres, length area enclosed regions and...
ABSTRACT Effector T-cells rely on integrins to drive adhesion and migration facilitate their immune function. The heterodimeric transmembrane integrin LFA-1 (αLβ2 integrin) regulates of effector through linkage the extracellular matrix with intracellular actin treadmill machinery. Here, we quantified velocity direction F-actin flow in migrating alongside single-molecule localisation LFA-1. Results showed that retrograde positively correlated immobile negatively T-cell velocity. Plasma...
Elucidating the mechanisms that controlled T cell activation requires visualization of spatial organization multiple proteins on submicron scale. Here, we use stoichiometrically accurate, multiplexed, single-molecule super-resolution microscopy (DNA-PAINT) to image nanoscale architecture primary inhibitor signaling pathway, Csk, and two binding partners implicated in its membrane association, PAG TRAF3. Combined with a newly developed co-clustering analysis framework, find Csk forms clusters...
Fluorescent d-amino acids (FDAAs) have previously been developed to enable in situ highlighting of locations bacterial cell wall growth. Most cells lie at the edge diffraction limit visible light; thus, resolving precise details peptidoglycan (PG) biosynthesis requires super-resolution microscopy after probe incorporation. Single molecule localization (SMLM) has stringent requirements on fluorophore photophysical properties and therefore remained challenging this context. Here, we report...
Abstract Until recently, single‐molecule localization microscopy (SMLM) was constrained to the study of fixed cells, limiting analysis structural characterization cell anatomy. The extension SMLM live‐cell imaging enables dynamic visualization molecular organization, paving way for more functional studies. If associated with novel quantification tools such as presented here, it has potential provide a unique insight into cellular machinery at nanoscale. While cluster conventional data sets...
Unlike conventional microscopy which produces pixelated images, SMLM data in the form of a list localization coordinates-a spatial point pattern (SPP). Often, such SPPs are analyzed using cluster analysis algorithms to quantify molecular clustering within, for example, plasma membrane. While is now well developed, techniques analyzing fibrous structures remain poorly explored.Here, we demonstrate statistical methodology, based on Ripley's K-function quantitatively assess 2D datasets. Using...
Molecular clustering at the plasma membrane has long been identified as a key process and is associated with regulating signalling pathways across cell types. Recent advances in microscopy, particular rise of super-resolution, have allowed experimental observation nanoscale molecular clusters membrane. However, modelling approaches capable recapitulating these observations are their infancy, partly because extremely complex array biophysical factors which influence distributions dynamics We...
Abstract Although single molecule localisation microscopy enables for the visualisation of cells nanoscale organisation, its dissemination remains limited mainly due to complexity associated imaging acquisition, impacting on outputs’ reliability and reproducibility. We propose here first all-in-one fully virtual environment SMLM acquisition: Virtual-SMLM , including on-the-fly interactivity real time display. It relies a novel realistic approach simulate fluorophores photo-physics based...
Abstract Effector T-cells rely on integrins to drive adhesion and migration facilitate their immune function. Heterodimeric transmembrane integrin LFA-1 (αLβ2) regulates through linkage of the extracellular matrix with intracellular actin treadmill machinery. We quantitated velocity direction F-actin flow in migrating alongside single molecule localisation LFA-1. Our results show that retrograde positively correlated immobile negatively T-cell velocity. Plasma membrane localised forms unique...
Abstract Single molecule localisation microscopy (SMLM) generates data in the form of Cartesian coordinates localised fluorophores. Cluster analysis is an attractive route for extracting biologically meaningful information from such and has been widely applied. Despite range developed cluster algorithms, there exists no consensus framework evaluation their performance. Here, we use a systematic approach based on two metrics, Adjusted Rand Index (ARI) Intersection over Union (IoU), to score...