Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
We present an efficient detection scheme for localization of Double Helix point-spread functions for 3D single-molecule localization microscopy or tracking. Using steerable filters, we extract both 2D position and lobe orientation (axial position) estimates using just 7 convolutions, orders of magnitude less than used in deep learning based approaches. For a complete SMLM analysis pipeline, we pair this detection with a fitter using an optimally parameterized double Gaussian model, and implement both as a plugin for the open source PYthon Microscopy Environment (PYME).
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC12393288 | PMC |
| http://dx.doi.org/10.1101/2025.08.14.670427 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Multiview Deep Learning Framework for Precise Prediction of Transcription Factor Binding Sites.
J Chem Inf Model
September 2025
Key Laboratory of Micro-nano Sensing and IoT of Wenzhou, Wenzhou Institute of Hangzhou Dianzi University, Wenzhou 325038, China.
Transcription factors (TFs) are essential proteins that regulate gene expression by specifically binding to transcription factor binding sites (TFBSs) within DNA sequences. Their ability to precisely control the transcription process is crucial for understanding gene regulatory networks, uncovering disease mechanisms, and designing synthetic biology tools. Accurate TFBS prediction, therefore, holds significant importance in advancing these areas of research.
View Article and Find Full Text PDFA Super-Resolution Spatial Atlas of SARS-CoV-2 Infection in Human Cells.
bioRxiv
August 2025
Department of Chemistry; Stanford University, Stanford, CA 94305 U.S.A.
The spatial organization of viral and host components dictates the course of infection, yet the nanoscale architecture of the SARS-CoV-2 life cycle remains largely uncharted. Here, we present a comprehensive super-resolution Atlas of SARS-CoV-2 infection, systematically mapping the localization of nearly all viral proteins and RNAs in human cells. This resource reveals that the viral main protease, nsp5, localizes to the interior of double-membrane vesicles (DMVs), challenging existing models and suggesting that polyprotein processing is a terminal step in replication organelle maturation.
View Article and Find Full Text PDFEfficient Double Helix Detection with Steerable Filters.
bioRxiv
August 2025
Department of Chemistry, Stanford University, Stanford, California 94305, USA.
We present an efficient detection scheme for localization of Double Helix point-spread functions for 3D single-molecule localization microscopy or tracking. Using steerable filters, we extract both 2D position and lobe orientation (axial position) estimates using just 7 convolutions, orders of magnitude less than used in deep learning based approaches. For a complete SMLM analysis pipeline, we pair this detection with a fitter using an optimally parameterized double Gaussian model, and implement both as a plugin for the open source PYthon Microscopy Environment (PYME).
View Article and Find Full Text PDFThe Mre11 nuclease is part of the highly conserved MRX complex involved in the repair of DNA double-strand breaks (DSBs). During meiosis in budding yeast, MRX is also required for the programmed induction of DSBs by Spo11, thereby initiating homologous recombination to promote accurate chromosome segregation. Recruitment of Mre11 to meiotic DSB sites depends on Rec114-Mei4 and Mer2 (RMM), which are thought to organize the meiotic DSB machinery by a mechanism involving biomolecular condensation.
View Article and Find Full Text PDFPraseodymium doped cerium oxide nanozyme as a functional analog of topoisomerase I.
J Inorg Biochem
December 2025
International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga s/n, 4715-330 Braga, Portugal.
Topoisomerases are essential hydrolases that facilitate the topological rearrangement of DNA by cleaving nucleic acid strands. Specifically, topoisomerase I (TOPO I) enhances DNA transcription by introducing single-strand breaks in the DNA double helix, relaxing supercoiled DNA, and catalyzing the subsequent re-ligation of the cleavage sites. However, the intricate catalytic mechanism of TOPO I has posed significant challenges for developing effective enzymatic mimics.
View Article and Find Full Text PDF