Publications associées à Nfinder: automatic inference of cell neighborhood in 2D and 3D using nuclear markers

Publications associées (23)

Structural basis of BAK sequestration by MCL-1 in apoptosis

Apoptosis controls cell fate, ensuring tissue homeostasis and promoting disease when dysregulated. The rate-limiting step in apoptosis is mitochondrial poration by the effector B cell lymphoma 2 (BCL-2) family proteins BAK and BAX, which are activated by i ...

2025

Exploiting Covalent Chemical Labeling with Self-Labeling Proteins

Kai Johnsson

The visualization and manipulation of proteins in live cells are critical for studying complex biological processes. Self-labeling proteins do so by enabling the specific and covalent attachment of synthetic probes, offering unprecedented flexibility in th ...

Annual Reviews2025

Significant reduction of cell invasiveness in nanoneedle insertion into a living cell with an electron-beam-deposited probe: impacts of probe geometry, speed and vibration

Marcos Penedo Garcia

Intracellular probing of living cells using atomic force microscopy (AFM) has advanced significantly, but it requires specially designed nanoprobes to achieve precision and minimize damage. The development of focused ion beam (FIB)-milled nanoprobes enable ...

2025

Lamellar Schwann Cells in the Pacinian Corpuscle Potentiate Vibration Perception

Graham Knott, Mary-Claude Croisier-Coeytaux, Jérôme Blanc, Stéphanie Clerc

Pacinian corpuscles are among the most sensitive mechanoreceptors found in vertebrates, and they are tuned to vibrations in the highest perceptible frequency range (100 to 2000 Hz). One of their anatomical hallmarks is the onion-like cell layers surroundin ...

AMER ASSOC ADVANCEMENT SCIENCE2025

Bioanode engineering for living solar cells

Charlotte Elisabeth Marie Roullier

Whole-cell biophotovoltaic (BPV) devices leverage photoautotrophic microorganisms like cyanobacteria to convert sunlight and water into bioelectricity. They are capable of growing on sequestered carbon dioxide (CO2), eliminating the need to add exogenous o ...

EPFL2025

Engineering Symmetry Breaking Interfaces by Nanoscale Structural-Energetics in Orthorhombic Perovskite Thin Films

Duncan Thomas Lindsay Alexander, Bernat Mundet

The atomic configuration of phases and their interfaces is fundamental to materials design and engineering. Here, we unveil a transition metal oxide interface, whose formation is driven by energetic influences─epitaxial tensile strain versus oxygen octahed ...

2025

Computational design of complex protein folds and soluble analogs of membrane proteins

Casper Alexander Goverde

Proteins are the molecular machines of life, driving essential biological processes such as enzymatic catalysis, cellular signaling, and immune responses. The ability to design entirely new proteins with desired structures and functions has immense implica ...

EPFL2025

Advanced imaging of gas diffusion layers: A comparison between focused ion beam scanning electron microscopy and X-ray computed tomography

Jan Van Herle, Hossein Pourrahmani

With the advances in clean technologies, the role of fuel cells and batteries is becoming increasingly vital. Proton exchange membrane fuel cells are known to be the best candidates for low-temperature and portable operations, such as hydrogen cars. The ef ...

2025

Passivating oxidation behavior of Ti0.12Al0.21B0.67 coatings investigated by scanning transmission electron microscopy and chemical environment dependent density functional theory simulations

Johann Michler

The oxidation behavior of stoichiometric Ti0.12Al0.21B0.67 coatings is investigated by scanning transmission electron microscopy (STEM) after oxidizing for 1, 4 and 8 h at 700 degrees C and at 800 and 900 degrees C. In the as deposited state, a similar to ...

PERGAMON-ELSEVIER SCIENCE LTD2025

A Multiscale Bayesian Approach to Quantification and Denoising of Energy-dispersive X-ray Data

Cécile Hébert, Duncan Thomas Lindsay Alexander, Pau Torruella Besa

Energy dispersive x-ray (EDX) spectrum imaging yields compositional information with a spatial resolution down to the atomic level. However, experimental limitations often produce extremely sparse and noisy EDX spectra. Under such conditions, every detecte ...

IOP Publishing Ltd2025

Bulk measurement of membrane permeability for random cyclic peptides in living cells to guide drug development

Nathan Moïse De Sadeleer, Christian Heinis, Alexander Lund Nielsen, Anne Sofie Luise Zarda, Rebecca Manuela Neeser

Cyclic peptides are attractive for drug discovery due to their excellent binding properties and the potential to cross cell membranes. However, by far not all cyclic peptides are cell permeable, and measuring or predicting their membrane permeability is no ...

Wiley2025

Hard x-ray grazing-incidence ptychography: large field-of-view nanostructure imaging with ultra-high surface sensitivity

Manuel Guizar Sicairos

The morphology and distribution of nanoscale structures, such as catalytic active nanoparticles and quantum dots on surfaces, have a significant impact on their function. Thus, the capability of monitoring these properties during manufacturing and operatio ...

Optica Publishing Group2024

Investigating the Effect of Misalignment on Membership Privacy in the White-box Setting

Ana-Maria Cretu

Machine learning models have been shown to leak sensitive information about their training datasets. Models are increasingly deployed on devices, raising concerns that white-box access to the model parameters increases the attack surface compared to black- ...

Privacy Enhancing Technologies Symposium Advisory Board2024

Nissl_6, Raw images for Machine learning for histological annotation and quantification of cortical layers

Julie Meystre

This dataset contains images (TIFF image data) of brain juvenile rats Wistar Han (P14) scanned immunostained slides by using an automated slide scanner (Olympus, VS120-L100, GER) equipped with a UPLSAPO 20x/0.75 air objective (Olympus, GER) and a Pike F5 ...

Zenodo2024

Mechanisms of axoneme and centriole elimination in Naegleria gruberi

Graham Knott, Pierre Gönczy, Coralie Busso, Mary-Claude Croisier-Coeytaux, Alexander Woglar, Friso Edsger Douma, Gabriela Garcia Rodriguez

The early branching eukaryote Naegleria gruberi can transform transiently from an amoeboid life form lacking centrioles and flagella to a flagellate life form where these elements are present, followed by reversion to the amoeboid state. The mechanisms imp ...

SPRINGERNATURE2024

Unraveling mitochondrial dynamics: exploring asymmetries and function through advanced microscopy

Julius Hans Bernd Winter

Still displaying characteristics of their bacterial origin, such as autonomous division, motility, and their own genome, mitochondria remain an elusive component of modern eukaryotes. They produce most of the cell's energy in the form of adenosine triphosp ...

EPFL2024

Computational drug development for membrane protein targets

Pierre Vogel, Henning Paul-Julius Stahlberg, Shuguang Yuan, Dongchun Ni, Babatunde Edukpe Ekundayo

The application of computational biology in drug development for membrane protein targets has experienced a boost from recent developments in deep learning-driven structure prediction, increased speed and resolution of structure elucidation, machine learni ...

2024

Revealing chromatin-specific functions of histone deacylases

Beat Fierz, Carlos Moreno Yruela

Histone deacylases are erasers of Nε-acyl-lysine post-translational modifications and have been targeted for decades for the treatment of cancer, neurodegeneration and other disorders. Due to their relatively promiscuous activity on peptide substrates in v ...

2024

Disentangling Multiple System Atrophy - Structural insights from alpha-synuclein fibrils and tissue pathology

Domenic Burger

Multiple System Atrophy (MSA) is an aggressive neurodegenerative disorder characterized by the formation of Glial Cytoplasmic Inclusions (GCI) containing alpha-synuclein (aSyn) fibrils in brain tissue. The fundamental causes for many neurodegenerative dise ...

EPFL2024

Gentle Rhodamines for Live-Cell Fluorescence Microscopy

Luc Reymond

Rhodamines have been continuously optimized in brightness, biocompatibility, and color to fulfill the demands of modern bioimaging. However, the problem of phototoxicity caused by the excited fluorophore under long-term illumination has been largely neglec ...

2024