Papers

Revision as of 14:57, 8 January 2014

Light Microscopy

How to get it right

• Cromey, D.W., 2010. Avoiding Twisted Pixels: Ethical Guidelines for the Appropriate Use and Manipulation of Scientific Digital Images
  Science and Engineering Ethics 16, pp. 639–667 source

• Pearson, Helen, 2007: The good, the bad and the ugly
  Nature 447, 138-140 (10 May 2007) source

• Pawley, Jim, 2000: The 39 Steps: A Cautionary Tale about “quantatative” 3D Fluorescence Microscopy
  BioTechniques 28-5:2-4 source

• Eisenstein, Michael, 2006: Something to see
  Nature 443, 1017-1021 (26 October 2006) source

Fluorescent Proteins

• Shcherbakova, D.M. et. al., 2013 Near-infrared fluorescent proteins for multicolor in vivo imaging
  Nature Methods 10, 751–754 (2013) source

• Shcherbakova, D.M. et. al., 2012 Red fluorescent proteins: advanced imaging applications and future design
  Angew Chem Int Ed Engl. 51(43):10724-38

• Nienhaus, G.U. et. al., 2008: Optimized and Far-Red-Emitting Variants of Fluorescent Protein eqFP611.
  Chem Biol. 2008 Mar;15(3):224-33. source

• Koushik, Srinagesh V. et. al. , 2006: Cerulean, Venus, and VenusY67C FRET Reference Standards
  Biophys J. 2006 December 15; 91(12): L99–L101. source

• Eisenstein, Michael, 2006: Helping cells to tell a colorful tale
  Nature Methods 3, 647 - 655 (01 Aug 2006) source

Techniques

• Davide Mazza, Kevin Braeckmans, Francesca Cella, Ilaria Testa, Dries Vercauteren, Jo Demeester, Stefaan S. De Smedt, Alberto Diaspro, 2008
  A New FRAP/FRAPa Method For 3-D Diffusion Measurements Based On Multi-photon Excitation Microscopy
  Biophys. J. BioFAST: First Published July 11, 2008. doi:10.1529/biophysj.108.133637 source

• Donnert, Gerald et al., 2006, Major signal increase in fluorescence microscopy through dark-state relaxation
  Nature Methods 4 (01), 81-86

• Frohn, J. T. et. al., 2001: Three-dimensional resolution enhancement in fluorescence microscopy by harmonic excitation
  Optics Letters, Vol. 26, Issue 11, pp. 828-830 source

• Göbel, Werner et. al., 2007: Imaging cellular network dynamics in three dimensions using fast 3D laser scanning
  Nature Methods - 4, 73 - 79 (2007) source

• Edward J. Botcherby, Rimas Juskaitis, Martin J. Booth, Tony Wilson, 2007: Aberration-free optical refocusing in high numerical aperture microscopy.
  Opt Lett. 2007 Jul 15;32(14):2007-9 source

Technical Tests

• Murray, John M. et. al., 2007: Evaluating performance in three-dimensional fluorescence microscopy
  Journal of Microscopy Volume 228 Issue 3 Page 390-405, December 2007 source

• Zucker, Robert M., 2006: Quality Assessment of Confocal Microscopy Slide Based Systems: Performance
  Cytometry Part A 69A:659–676 (2006) source

• Zucker, Robert M., 2006: Quality Assessment of Confocal Microscopy Slide-Based Systems: Instability
  Cytometry Part A 69A:677–690 (2006) source

• Zucker, Robert M., 2007: Reliability of confocal microscopy spectral imaging systems: Use of multispectral beads.
  Cytometry A. 2007 Jan 31 source

Image Processing and Analysis

Algorithms

• Mitchel, J.A., Martin, I.S., Hoffman-Kim, D., 2013. Neurient: An algorithm for automatic tracing of confluent neuronal images to determine alignment
  Journal of Neuroscience Methods 214, pp. 210–222 source

• Meijering, E., Dzyubachyk, O., Smal, I., 2012. Methods for Cell and Particle Tracking,
  in: Methods in Enzymology. Elsevier, pp. 183–200 source

• Dima, A.A. et. al., 2011. Comparison of segmentation algorithms for fluorescence microscopy images of cells
  Cytometry Part A 79, pp. 545–559 source

• Padmanabhan, K. et. al., 2010: A novel algorithm for optimal image thresholding of biological data
  Journal of Neuroscience Methods, 193:2, pp. 380-384 source

Colocalization

• Dunn, K.W., Kamocka, M.M., McDonald, J.H., 2011. A practical guide to evaluating colocalization in biological microscopy
  American Journal of Physiology-Cell Physiology 300, C723–C742 source

• Bolte, S. et. al., 2006: A guided tour into subcellular colocalization analysis in light microscopy
  Journal of Microscopy, Vol. 224, Pt 3 December 2006, pp. 213–232 source
  • Good paper to start with if you want to learn more about colocalization. Covers all relevant points.

• Costes, Sylvain V. et. al., 2004: Automatic and Quantitative Measurement of Protein-Protein Colocalization in Live Cells
  Biophysical Journal Volume 86 June 2004 3993–4003 source

• Manders, E.M.M. et. al., 1993: Measurement of co-localization of objects in dual-color confocal images
  Journal of Microscopy, Vol. 169, Pt 3, March 1993, pp. 375-382

• Manders, E.M.M. et. al., 1992: Dynamics of three-dimensional replication patterns during the S-phase, analyzed by double labelling of DNA and confocal microscopy
  Journal of Cell Science 103, 857-862 (1992)