Among the many super-resolution techniques for microscopy, single-molecule localization microscopy methods are widely used. This technique raises the difficult question of precisely localizing fluorophores from a blurred, under-resolved, and noisy acquisition. In this work, we focus on the grid-based approach in the context of a high density of fluorophores formalized by a ℓ least-square term and sparsity term modeled with ℓ pseudo-norm. We consider both the constrained formulation and the penalized formulation. Based on recent results, we formulate the ℓ pseudo-norm as a convex minimization problem. This is done by introducing an auxiliary variable. An exact biconvex reformulation of the ℓ - ℓ constrained and penalized problems is proposed with a minimization algorithm. The algorithms, named CoBic (Constrained Biconvex) and PeBic (Penalized Biconvex) are applied to the problem of single-molecule localization microscopy and we compare the results with other recently proposed methods.
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http://dx.doi.org/10.1364/BOE.381666 | DOI Listing |
Protein Sci
February 2025
IRR Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK.
Super-resolution microscopy has revolutionized biological imaging, enabling the visualization of structures at the nanometer length scale. Its application in live cells, however, has remained challenging. To address this, we adapted LIVE-PAINT, an approach we established in yeast, for application in live mammalian cells.
View Article and Find Full Text PDFSci Adv
January 2025
Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.
Understanding chromatin organization requires integrating measurements of genome connectivity and physical structure. It is well established that cohesin is essential for TAD and loop connectivity features in Hi-C, but the corresponding change in physical structure has not been studied using electron microscopy. Pairing chromatin scanning transmission electron tomography with multiomic analysis and single-molecule localization microscopy, we study the role of cohesin in regulating the conformationally defined chromatin nanoscopic packing domains.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
January 2025
Faculty of Technical Chemistry, Institute of Chemical Technologies and Analytics, Technische Universität Wien, Vienna 1060, Austria.
Atomic force microscopy-infrared spectroscopy (AFM-IR) is a photothermal scanning probe technique that combines nanoscale spatial resolution with the chemical analysis capability of mid-infrared spectroscopy. Using this hybrid technique, chemical identification down to the single molecule level has been demonstrated. However, the mechanism at the heart of AFM-IR, the transduction of local photothermal heating to cantilever deflection, is still not fully understood.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
January 2025
Department of Chemical Engineering, Stanford University, Stanford, CA 94305.
The crowded bacterial cytoplasm is composed of biomolecules that span several orders of magnitude in size and electrical charge. This complexity has been proposed as the source of the rich spatial organization and apparent anomalous diffusion of intracellular components, although this has not been tested directly. Here, we use biplane microscopy to track the 3D motion of self-assembled bacterial genetically encoded multimeric nanoparticles (bGEMs) with tunable size (20 to 50 nm) and charge (-3,240 to +2,700 e) in live cells.
View Article and Find Full Text PDFMov Disord
January 2025
Brain and Mind Centre, The University of Sydney, Sydney, New South Wales, Australia.
Background: Parkinson's disease (PD) is the most common neurodegenerative movement disease. Human endogenous retroviruses (HERVs) are proviral remnants of ancient retroviral infection of germ cells that now constitute about 8% of the human genome. Under certain disease conditions, HERV genes are activated and partake in the disease process.
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