ColiCoords: A Python package for the analysis of bacterial fluorescence microscopy data
Published 2019 View Full Article
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Title
ColiCoords: A Python package for the analysis of bacterial fluorescence microscopy data
Authors
Keywords
Bright field microscopy, Fluorescence imaging, Photons, Fluorescence microscopy, Neural networks, Bacteria, Cartesian coordinates, Image analysis
Journal
PLoS One
Volume 14, Issue 6, Pages e0217524
Publisher
Public Library of Science (PLoS)
Online
2019-06-20
DOI
10.1371/journal.pone.0217524
References
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- (2017) Alexandre W. Bisson-Filho et al. SCIENCE
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- (2017) Jacob S Lewis et al. eLife
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- (2017) Lisa E. Lamberte et al. Nature Microbiology
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- (2016) Feng Yang et al. MOLECULAR MICROBIOLOGY
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- (2016) Stella Stylianidou et al. MOLECULAR MICROBIOLOGY
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- (2016) Anne Plochowietz et al. NUCLEIC ACIDS RESEARCH
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- (2016) Johannes P. Schneider et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
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- (2016) Britta Barlag et al. Scientific Reports
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- ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging
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- (2014) Helen Shen NATURE
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- (2014) S. J. Holden et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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- (2013) Robert Crawford et al. BIOPHYSICAL JOURNAL
- Measuring mRNA copy number in individual Escherichia coli cells using single-molecule fluorescent in situ hybridization
- (2013) Samuel O Skinner et al. Nature Protocols
- Exploring bacterial cell biology with single-molecule tracking and super-resolution imaging
- (2013) Andreas Gahlmann et al. NATURE REVIEWS MICROBIOLOGY
- Amino Acids for Diels-Alder Reactions in Living Cells
- (2012) Tilman Plass et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
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