Quantitative Colocalisation Imaging: Concepts, Measurements, and Pitfalls

[1]  Haian Fu,et al.  Protein-protein interactions : methods and applications , 2004 .

[2]  P. Schwille,et al.  Fluorescence cross-correlation spectroscopy in living cells , 2006, Nature Methods.

[3]  Michael P Stryker,et al.  A method for measuring colocalization of presynaptic markers with anatomically labeled axons using double label immunofluorescence and confocal microscopy , 2000, Journal of Neuroscience Methods.

[4]  J. Gelles,et al.  Viewing dynamic assembly of molecular complexes by multi-wavelength single-molecule fluorescence. , 2006, Biophysical journal.

[5]  M. Gustafsson Nonlinear structured-illumination microscopy: wide-field fluorescence imaging with theoretically unlimited resolution. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Santiago Costantino,et al.  A guide to accurate fluorescence microscopy colocalization measurements. , 2006, Biophysical journal.

[7]  K. Sullivan,et al.  Green Fluorescent Proteins , 1999 .

[8]  J. Lippincott-Schwartz,et al.  Imaging Intracellular Fluorescent Proteins at Nanometer Resolution , 2006, Science.

[9]  Weidong Yang,et al.  Visualizing single molecules interacting with nuclear pore complexes by narrow-field epifluorescence microscopy. , 2006, Methods.

[10]  Brian J. Bacskai,et al.  Amyloid Precursor Protein Associates with a Nicastrin-Dependent Docking Site on the Presenilin 1–γ-Secretase Complex in Cells Demonstrated by Fluorescence Lifetime Imaging , 2003, The Journal of Neuroscience.

[11]  D Zicha,et al.  Quantitative fluorescence resonance energy transfer (FRET) measurement with acceptor photobleaching and spectral unmixing , 2004, Journal of microscopy.

[12]  Christian Eggeling,et al.  Breaking the diffraction barrier in fluorescence microscopy at low light intensities by using reversibly photoswitchable proteins. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Rainer Heintzmann,et al.  High-resolution colocalization of single dye molecules by fluorescence lifetime imaging microscopy. , 2002, Analytical chemistry.

[14]  M K Cheezum,et al.  Quantitative comparison of algorithms for tracking single fluorescent particles. , 2001, Biophysical journal.

[15]  J. Goedhart,et al.  Multiparameter Imaging for the Analysis of Intracellular Signaling , 2005, Chembiochem : a European journal of chemical biology.

[16]  Frank Kirchhoff,et al.  Expression of reef coral fluorescent proteins in the central nervous system of transgenic mice , 2005, Molecular and Cellular Neuroscience.

[17]  N. Ropert,et al.  Systematic colocalization errors between acridine orange and EGFP in astrocyte vesicular organelles. , 2007, Biophysical journal.

[18]  G. Patterson,et al.  Use of the green fluorescent protein and its mutants in quantitative fluorescence microscopy. , 1997, Biophysical journal.

[19]  Fred A. Kruse,et al.  The Spectral Image Processing System (SIPS) - Interactive visualization and analysis of imaging spectrometer data , 1993 .

[20]  L Landmann,et al.  Deconvolution improves colocalization analysis of multiple fluorochromes in 3D confocal data sets more than filtering techniques , 2002, Journal of microscopy.

[21]  R. Lynch,et al.  Modulation of hexokinase association with mitochondria analyzed with quantitative three-dimensional confocal microscopy , 1991, The Journal of cell biology.

[22]  R. Lowy Evaluation of triple‐band filters for quantitative epifluorescence microscopy , 1995, Journal of microscopy.

[23]  D. Schild,et al.  Sizing-up finite fluorescent particles with nanometer-scale precision by convolution and correlation image analysis , 2005, European Biophysics Journal.

[24]  P. G. Penarrubia,et al.  Quantitative analysis of the factors that affect the determination of colocalization coefficients in dual-color confocal images , 2005, IEEE Transactions on Image Processing.

[25]  W. Webb,et al.  Automated detection and tracking of individual and clustered cell surface low density lipoprotein receptor molecules. , 1994, Biophysical journal.

[26]  W. Denk,et al.  Two-photon imaging to a depth of 1000 microm in living brains by use of a Ti:Al2O3 regenerative amplifier. , 2003, Optics letters.

[27]  Chang‐Deng Hu,et al.  Visualization of interactions among bZIP and Rel family proteins in living cells using bimolecular fluorescence complementation. , 2002, Molecular cell.

[28]  S. Hell,et al.  Nanoscale resolution in GFP-based microscopy , 2006, Nature Methods.

[29]  D. Demandolx,et al.  Multicolour analysis and local image correlation in confocal microscopy , 1997 .

[30]  Henrik Flyvbjerg,et al.  A non-Gaussian distribution quantifies distances measured with fluorescence localization techniques. , 2006, Biophysical journal.

[31]  R. Truant,et al.  Practical three color live cell imaging by widefield microscopy , 2006, Biological Procedures Online.

[32]  Paul R. Selvin,et al.  Myosin V Walks Hand-Over-Hand: Single Fluorophore Imaging with 1.5-nm Localization , 2003, Science.

[33]  D. Axelrod,et al.  Selective imaging of surface fluorescence with very high aperture microscope objectives. , 2001, Journal of biomedical optics.

[34]  X Michalet,et al.  Ultrahigh-resolution colocalization of spectrally separable point-like fluorescent probes. , 2001, Methods.

[35]  Jun-ya Shoji,et al.  Vacuolar Membrane Dynamics in the Filamentous Fungus Aspergillus oryzae , 2006, Eukaryotic Cell.

[36]  T. Hébert,et al.  Detecting and imaging protein-protein interactions during G protein-mediated signal transduction in vivo and In situ by using fluorescence-based techniques , 2006, Cell Biochemistry and Biophysics.

[37]  Paul Wintz,et al.  Digital image processing (2nd ed.) , 1987 .

[38]  P. Stanton,et al.  BDNF increases release probability and the size of a rapidly recycling vesicle pool within rat hippocampal excitatory synapses , 2006, The Journal of physiology.

[39]  E Neher,et al.  Optimizing imaging parameters for the separation of multiple labels in a fluorescence image , 2004, Journal of microscopy.

[40]  J. Lübke,et al.  FM1-43 dye ultrastructural localization in and release from frog motor nerve terminals. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[41]  Fast and Precise Protein Tracking Using Repeated Reversible Photoactivation , 2006, Traffic.

[42]  Hjalmar Brismar,et al.  Fluorescence lifetime measurements in confocal microscopy of neurons labeled with multiple fluorophores , 1997, Nature Biotechnology.

[43]  D. F. Ogletree,et al.  Probing the interaction between single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor , 1996, Summaries of Papers Presented at the Quantum Electronics and Laser Science Conference.

[44]  Colin J. R. Sheppard,et al.  Signal-to-Noise in Confocal Microscopes , 1995 .

[45]  S. Ekker,et al.  Three-color imaging using fluorescent proteins in living zebrafish embryos. , 2001, BioTechniques.

[46]  R. Heim,et al.  Understanding structure-function relationships in the Aequorea victoria green fluorescent protein. , 1999, Methods in cell biology.

[47]  C. Furlanello,et al.  New image processing tools for GRASS , 2004 .

[48]  T. Meyer,et al.  Compartmentalized IgE Receptor–mediated Signal Transduction in Living Cells , 1997, The Journal of cell biology.

[49]  T. Kerppola,et al.  Visualization of molecular interactions by fluorescence complementation , 2006, Nature Reviews Molecular Cell Biology.

[50]  R. Tsien,et al.  The Fluorescent Toolbox for Assessing Protein Location and Function , 2006, Science.

[51]  Hsin-Chih Yeh,et al.  Single-molecule detection and probe strategies for rapid and ultrasensitive genomic detection. , 2005, Current pharmaceutical biotechnology.

[52]  M. D'Esposito,et al.  A dual mechanism controlling the localization and function of exocytic v-SNAREs , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[53]  J. Spudich,et al.  Single molecule high-resolution colocalization of Cy3 and Cy5 attached to macromolecules measures intramolecular distances through time. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[54]  W. Betz,et al.  Imaging exocytosis and endocytosis , 1996, Current Opinion in Neurobiology.

[55]  Oliver Griesbeck,et al.  Fluorescent proteins as sensors for cellular functions , 2004, Current Opinion in Neurobiology.

[56]  T. Zimmermann Spectral imaging and linear unmixing in light microscopy. , 2005, Advances in biochemical engineering/biotechnology.

[57]  Michael D. Mason,et al.  Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. , 2006, Biophysical journal.

[58]  S. Rhodes,et al.  Characterization and imaging of A6 epithelial cell clones expressing fluorescently labeled ENaC subunits. , 2001, American journal of physiology. Cell physiology.

[59]  A. Smallcombe,et al.  Multicolor imaging: the important question of co-localization. , 2001, BioTechniques.

[60]  Atsushi Miyawaki,et al.  Innovations in the Imaging of Brain Functions using Fluorescent Proteins , 2005, Neuron.

[61]  J. Aten,et al.  Measurement of co‐localization of objects in dual‐colour confocal images , 1993, Journal of microscopy.

[62]  Masafumi Oshiro,et al.  Cooled vs. intensified vs. electron bombardment CCD cameras--applications and relative advantages. , 2003, Methods in cell biology.

[63]  K. Pogliano,et al.  An in vivo membrane fusion assay implicates SpoIIIE in the final stages of engulfment during Bacillus subtilis sporulation. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[64]  T. Williams,et al.  Fluorescence labeling, purification, and immobilization of a double cysteine mutant calmodulin fusion protein for single-molecule experiments. , 2004, Analytical biochemistry.

[65]  L. Personnaz,et al.  Detecting fluorescent protein expression and co-localisation on single secretory vesicles with linear spectral unmixing , 2006, European Biophysics Journal.

[66]  J Strackee,et al.  Largest contour segmentation: a tool for the localization of spots in confocal images. , 1996, Cytometry.

[67]  Jerome Mertz,et al.  Epifluorescence collection in two-photon microscopy. , 2002, Applied optics.

[68]  Liming Ying,et al.  Ultrasensitive coincidence fluorescence detection of single DNA molecules. , 2003, Analytical chemistry.

[69]  N O Petersen,et al.  An internalization-competent influenza hemagglutinin mutant causes the redistribution of AP-2 to existing coated pits and is colocalized with AP-2 in clathrin free clusters. , 1999, Biochemistry.

[70]  W. Stühmer,et al.  Calcium regulates exocytosis at the level of single vesicles , 2003, Nature Neuroscience.

[71]  W. Betz,et al.  Using FM1-43 to study neuropeptide granule dynamics and exocytosis. , 2004, Methods.

[72]  T. Miyashita Confocal microscopy for intracellular co-localization of proteins. , 2004, Methods in molecular biology.

[73]  P. Schwille,et al.  Dual-color fluorescence cross-correlation spectroscopy for multicomponent diffusional analysis in solution. , 1997, Biophysical journal.

[74]  H. Okano,et al.  Use of TH-EGFP transgenic mice as a source of identified dopaminergic neurons for physiological studies in postnatal cell culture , 2005, Journal of Neuroscience Methods.

[75]  R. Uhl,et al.  Instrumentation for multiwavelengths excitation imaging , 1996, Journal of Neuroscience Methods.

[76]  Dirk-Peter Herten,et al.  High-resolution colocalization of single molecules within the resolution gap of far-field microscopy. , 2005, Chemphyschem : a European journal of chemical physics and physical chemistry.

[77]  J. Gustafsson,et al.  Evidence for colocalization of glucocorticoid receptor with cytoplasmic microtubules in human gingival fibroblasts, using two different monoclonal anti-GR antibodies, confocal laser scanning microscopy and image analysis , 1991, The Journal of Steroid Biochemistry and Molecular Biology.

[78]  S. Lemeer,et al.  The AP-2 Complex Is Excluded from the Dynamic Population of Plasma Membrane-associated Clathrin* , 2003, Journal of Biological Chemistry.

[79]  M. Wessendorf,et al.  Which fluorophore is brightest? A comparison of the staining obtained using fluorescein, tetramethylrhodamine, lissamine rhodamine, texas red, and cyanine 3.18 , 1992, Histochemistry.

[80]  Anlian Qu,et al.  Three-dimensional tracking of single secretory granules in live PC12 cells. , 2004, Biophysical journal.

[81]  G J Brakenhoff,et al.  Dynamics of three-dimensional replication patterns during the S-phase, analysed by double labelling of DNA and confocal microscopy. , 1992, Journal of cell science.

[82]  J. Piehler New methodologies for measuring protein interactions in vivo and in vitro. , 2005, Current opinion in structural biology.

[83]  P. Matula,et al.  An efficient algorithm for measurement and correction of chromatic aberrations in fluorescence microscopy , 2000, Journal of microscopy.

[84]  M Wahl,et al.  Time-resolved confocal fluorescence imaging and spectrocopy system with single molecule sensitivity and sub-micrometer resolution. , 2004, Current pharmaceutical biotechnology.

[85]  Christophe Zimmer,et al.  Segmenting and tracking fluorescent cells in dynamic 3-D microscopy with coupled active surfaces , 2005, IEEE Transactions on Image Processing.

[86]  D. P. Shrestha,et al.  Analysis and classification of hyperspectral data for mapping land degradation: An application in southern Spain , 2005 .

[87]  Nathan C Shaner,et al.  A guide to choosing fluorescent proteins , 2005, Nature Methods.

[88]  J. Schmid,et al.  Application of spectral imaging microscopy in cytomics and fluorescence resonance energy transfer (FRET) analysis , 2004, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[89]  Pasi Fränti,et al.  Compression of map images by multilayer context tree modeling , 2005, IEEE Transactions on Image Processing.

[90]  Martin Oheim,et al.  Multiple stimulation-dependent processes regulate the size of the releasable pool of vesicles , 1999, European Biophysics Journal.

[91]  R. Cherry,et al.  Detecting and quantifying colocalization of cell surface molecules by single particle fluorescence imaging. , 2003, Biophysical journal.

[92]  Petra Schwille,et al.  Triple-color coincidence analysis: one step further in following higher order molecular complex formation. , 2004, Biophysical journal.

[93]  Jerome Mertz,et al.  Two-photon microscopy in brain tissue: parameters influencing the imaging depth , 2001, Journal of Neuroscience Methods.

[94]  Philip S Low,et al.  Evaluation of disulfide reduction during receptor-mediated endocytosis by using FRET imaging , 2006, Proceedings of the National Academy of Sciences.

[95]  Richard A Neher,et al.  Applying spectral fingerprinting to the analysis of FRET images , 2004, Microscopy research and technique.