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Detection efficiency in total internal reflection fluorescence microscopy

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Correlative light and volume electron microscopy to study brain development

Graham Knott

Recent advances in volume electron microscopy (EM) have been driving our thorough understanding of the brain architecture. Volume EM becomes increasingly powerful when cells and their subcellular structures that are imaged in light microscopy are correlate ...

OXFORD UNIV PRESS2023

Microfluidic devices for automated analysis of ingested bacteria in the Caenorhabditis elegans intestine

Farzad Rezaeianaran

In this thesis, we explored on-chip high-resolution imaging of the fate of intestinal bacteria and bacterial products in Caenorhabditis elegans (C. elegans). In the first part, we carried out high-resolution z-stack fluorescent imaging of Red Fluorescent P ...

EPFL2023

In Situ and Time-Resolved Transmission Electron Microscopy of Nanoscale Processes

Chengcheng Yan

Observing the fast dynamics of nanoscale systems is crucial in order to understand and ultimately control their behavior. Characterizing these dynamic processes requires techniques with atomic spatial resolution and a temporal resolution that matches the t ...

EPFL2023

Stain-free identification of cell nuclei using tomographic phase microscopy in flow cytometry

Demetri Psaltis, Joowon Lim

The accurate identification of the three-dimensional quantitative shape of a cell nucleus is now possible without fluorescent staining by applying computational segmentation to refractive index tomograms recorded in the flow cytometry mode. ...

Nature Publishing Group2022

Amplitude and phase reconstruction for Low-Energy Electron Holography of individual proteins

Hannah Julia Ochner

Single-molecule imaging methods are of importance in structural biology, and specifically in the imaging of proteins, since they can elucidate conformational variability and structural changes that might be lost in imaging methods relying on averaging proc ...

EPFL2022

Single molecule fluorescence and phosphorescence studies using a scanning tunneling microscope

Abhishek Grewal

This thesis investigates novel single-molecule luminescence phenomena at their inherent, sub-molecular length scale. The microscopic understanding of luminescence processes will be crucial for the continued improvement of organic optoelectronic and semicon ...

EPFL2022

Event-driven acquisition for content-enriched microscopy

Suliana Manley, Dora Mahecic, Martin Weigert, Juliette Griffie, Chen Zhang, Willi Leopold Stepp

Event-driven acquisition uses neural-network-based recognition of specific biological events to trigger switching between slow and fast super-resolution imaging, enriching the capture of interesting events with high spatiotemporal resolution. A common goal ...

Nature Publishing Group2022

Multidisciplinary Investigation of the Gut-Brain Ecosystem in a Model of Alzheimer's Disease

Arielle Louise Planchette

The search for an understanding of the causal elements that lead to neurodegenerative diseases has motivated researchers for decades. Today, Alzheimer's disease is the most prevalent form of dementia and affects approximately fifty million people worldwide ...

EPFL2022

Carbon K-edge x-ray emission spectroscopy of gas phase ethylenic molecules

Majed Chergui, Camila Bacellar Cases Da Silveira, Rebecca Ann Ingle, Luca Longetti, Thomas Roland Barillot

We report on the C K-edge x-ray absorption spectra and the resonant (RXES) and non-resonant (NXES) x-ray emission spectra of ethylene, allene and butadiene in the gas phase. The RXES and NXES show clear differences for the different molecules. Overall both ...

IOP Publishing2022

Plasmon-induced near-infrared fluorescence enhancement of single-walled carbon nanotubes

Giulia Tagliabue, Ardemis Anoush Boghossian, Shang-Jung Wu, Alessandra Antonucci, Theodoros Tsoulos, Amirmostafa Amirjani, Sayyed Hashem Sajjadi

Single-walled carbon nanotubes (SWCNTs) emit near-infrared (NIR) fluorescence that is ideal for optical sensing. However, the low quantum yields diminish the sensor’s signal-to-noise ratio and limits the penetration depths for in vivo measurements. In this ...

2022

Ultrafast Transverse Modulation of Free Electrons by Interaction with Shaped Optical Fields

Phoebe Marie Tengdin, Fabrizio Carbone, Thomas La Grange, Ivan Madan, Giovanni Maria Vanacore, Simone Gargiulo, Francesco Barantani, Alexey Sapozhnik, Veronica Leccese

Spatiotemporal electron-beam shaping is a bold frontier of electron microscopy. Over the past decade, shaping methods evolved from static phase plates to low-speed electrostatic and magnetostatic displays. Recently, a swift change of paradigm utilizing lig ...

AMER CHEMICAL SOC2022

Fluorescent D-Amino Acids for Super-resolution Microscopy of the Bacterial Cell Wall

Mischa André Meyer, Faustine Ambroisine Charline Ryckebusch, Suliana Manley, Luc Reymond, Chen Zhang, Juliette Griffie, Willi Leopold Stepp, Ophélie Rutschmann, Jiangtao Qiao

Fluorescent D-amino acids (FDAAs) have previ-ously been developed to enable in situ highlighting of locations of bacterial cell wall growth. Most bacterial cells lie at the edge of the diffraction limit of visible light; thus, resolving the precise details ...

2022

Nonlinear Inverse Problems in Quantitative Phase Imaging

Thanh-An Michel Pham

The topic of this thesis is the development of new algorithmic reconstruction methods for quantitative phase imaging (QPI). In the past decade, advanced QPI has emerged as a valuable tool to study label-free biological samples and uncover their 3D structur ...

EPFL2022

Advanced Techniques in Optical Diffraction Tomography

Ahmed Bassam Sayed Ayoub Mohamed Emam

In this thesis, we study the 3 challenges described above. First, we study different reconstruction techniques and assess the fidelity of each reconstruction results by means of structured illumination and phase conjugation. By reconstructing the 3D refrac ...

EPFL2022

Characterization of Pseudomonas aeruginosa mechanosensing through label-free imaging of type IV pili

Lorenzo Anton-Louis Talà

Bacteria are ubiquitously found in all sorts of environment. They're found in the ocean, soil, or even in our guts or on our skin. Independently of their niche, they can transition from a planktonic state were they freely swim in an aqueous environment to ...

EPFL2022