Papers
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* Pearson, Helen, 2007: ''The good, the bad and the ugly''<br>Nature 447, 138-140 (10 May 2007) [http://www.nature.com/nature/journal/v447/n7141/full/447138a.html source] | * Pearson, Helen, 2007: ''The good, the bad and the ugly''<br>Nature 447, 138-140 (10 May 2007) [http://www.nature.com/nature/journal/v447/n7141/full/447138a.html source] | ||
− | * | + | * Brown, C.M., 2007: ''Fluorescence microscopy - avoiding the pitfalls''<br>J Cell Sci 120, 1703-1705 [http://jcs.biologists.org/content/120/10/1703.full source] |
* Eisenstein, Michael, 2006: ''Something to see''<br>Nature 443, 1017-1021 (26 October 2006) [http://www.nature.com/nature/journal/v443/n7114/full/4431017a.html source] | * Eisenstein, Michael, 2006: ''Something to see''<br>Nature 443, 1017-1021 (26 October 2006) [http://www.nature.com/nature/journal/v443/n7114/full/4431017a.html source] | ||
+ | |||
+ | * Pawley, Jim, 2000: ''The 39 Steps: A Cautionary Tale about “quantatative” 3D Fluorescence Microscopy''<br>BioTechniques 28-5:2-4 [http://www.zoology.wisc.edu/faculty/Paw/pdfs/The_39_Steps_corrected.pdf source] | ||
=== Fluorescent Proteins === | === Fluorescent Proteins === | ||
Line 32: | Line 34: | ||
=== Techniques === | === Techniques === | ||
− | |||
− | * | + | * Becker, W., 2012: ''Fluorescence lifetime imaging – techniques and applications''<br>J Microsc. 247(2):119-36 [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2818.2012.03618.x/full source] |
− | * | + | * Weber, M. et.al., 2011: ''Light sheet microscopy for real-time developmental biology''<br>Curr Opin Genet Dev. 21(5):566-72 [http://www.sciencedirect.com/science/article/pii/S0959437X11001444 source] |
+ | |||
+ | * Truong, T.V. et. al., 2011: ''Deep and fast live imaging with two-photon scanned light-sheet microscopy''<br>Nature Methods 8, 757–760 [http://www.nature.com/nmeth/journal/v8/n9/full/nmeth.1652.html source] | ||
+ | |||
+ | * Min, W. et. al., 2011: ''Coherent nonlinear optical imaging: beyond fluorescence microscopy''<br>Annu Rev Phys Chem. 62:507-30 [http://www.annualreviews.org/doi/full/10.1146/annurev.physchem.012809.103512 source] | ||
+ | |||
+ | * Hell, S.W., 2009: ''Microscopy and its focal switch''<br>Nature Methods 6, 24 - 32 [http://www.nature.com/nmeth/journal/v6/n1/full/nmeth.1291.html source] | ||
+ | |||
+ | * Evans, C.L., et. al. 2008: ''Coherent Anti-Stokes Raman Scattering Microscopy: Chemical Imaging for Biology and Medicine''<br> Annu Rev Anal Chem 1:883-909 [http://www.annualreviews.org/doi/full/10.1146/annurev.anchem.1.031207.112754?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dpubmed source] | ||
+ | |||
+ | * Mazza, D. et. al., 2008:''A New FRAP/FRAPa Method For 3-D Diffusion Measurements Based On Multi-photon Excitation Microscopy''<br>Biophys J. 95(7):3457-69 [http://www.sciencedirect.com/science/article/pii/S0006349508784881 source] | ||
* Göbel, Werner et. al., 2007: ''Imaging cellular network dynamics in three dimensions using fast 3D laser scanning''<br>Nature Methods - 4, 73 - 79 (2007) [http://www.nature.com/nmeth/journal/v4/n1/abs/nmeth989.html;jsessionid=E707571DEBF996B20E6385F9D6346239 source] | * Göbel, Werner et. al., 2007: ''Imaging cellular network dynamics in three dimensions using fast 3D laser scanning''<br>Nature Methods - 4, 73 - 79 (2007) [http://www.nature.com/nmeth/journal/v4/n1/abs/nmeth989.html;jsessionid=E707571DEBF996B20E6385F9D6346239 source] | ||
− | * Edward J. Botcherby, Rimas Juskaitis, Martin J. Booth, Tony Wilson, 2007: ''Aberration-free optical refocusing in high numerical aperture microscopy.''<br>Opt Lett. | + | * Edward J. Botcherby, Rimas Juskaitis, Martin J. Booth, Tony Wilson, 2007: ''Aberration-free optical refocusing in high numerical aperture microscopy.''<br>Opt Lett. 32(14):2007-9 [http://www.opticsinfobase.org/abstract.cfm?URI=ol-32-14-2007 source] |
+ | |||
+ | * Donnert, Gerald et al., 2006, ''Major signal increase in fluorescence microscopy through dark-state relaxation''<br>Nature Methods 4 (01), 81-86 | ||
+ | |||
+ | * Frohn, J. T. et. al., 2001: ''Three-dimensional resolution enhancement in fluorescence microscopy by harmonic excitation''<br>Optics Letters 26 (11), 828-830 [http://www.opticsinfobase.org/abstract.cfm?URI=ol-26-11-828 source] | ||
=== Technical Tests === | === Technical Tests === | ||
+ | |||
+ | * Cole, R.W. et. al., 2011: ''Measuring and interpreting point spread functions to determine confocal microscope resolution and ensure quality control''<br>Nat Protoc. 6(12):1929-41 [http://www.nature.com/nprot/journal/v6/n12/full/nprot.2011.407.html source] | ||
* Murray, John M. et. al., 2007: ''Evaluating performance in three-dimensional fluorescence microscopy''<br>Journal of Microscopy Volume 228 Issue 3 Page 390-405, December 2007 [http://www.blackwell-synergy.com/doi/abs/10.1111/j.1365-2818.2007.01861.x source] | * Murray, John M. et. al., 2007: ''Evaluating performance in three-dimensional fluorescence microscopy''<br>Journal of Microscopy Volume 228 Issue 3 Page 390-405, December 2007 [http://www.blackwell-synergy.com/doi/abs/10.1111/j.1365-2818.2007.01861.x source] | ||
Line 52: | Line 69: | ||
* Zucker, Robert M., 2007: ''Reliability of confocal microscopy spectral imaging systems: Use of multispectral beads.''<br>Cytometry A. 2007 Jan 31 [http://lib.bioinfo.pl/pmid:17266146 source] | * Zucker, Robert M., 2007: ''Reliability of confocal microscopy spectral imaging systems: Use of multispectral beads.''<br>Cytometry A. 2007 Jan 31 [http://lib.bioinfo.pl/pmid:17266146 source] | ||
+ | * Zucker, Robert M., 2001: ''Evaluation of confocal microscopy system performance.''<br> Cytometry 44(4):273-94 [http://onlinelibrary.wiley.com/doi/10.1002/1097-0320%2820010801%2944:4%3C273::AID-CYTO1120%3E3.0.CO;2-N/abstract;jsessionid=794C22F761413F89B2EC95B39E6406DE.f01t04 source] | ||
== Image Processing and Analysis == | == Image Processing and Analysis == |
Latest revision as of 11:57, 6 February 2014
Contents |
[edit] Light Microscopy
[edit] 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
- Brown, C.M., 2007: Fluorescence microscopy - avoiding the pitfalls
J Cell Sci 120, 1703-1705 source
- Eisenstein, Michael, 2006: Something to see
Nature 443, 1017-1021 (26 October 2006) source
- Pawley, Jim, 2000: The 39 Steps: A Cautionary Tale about “quantatative” 3D Fluorescence Microscopy
BioTechniques 28-5:2-4 source
[edit] Fluorescent Proteins
- Shcherbakova, D.M. et. al., 2013 Near-infrared fluorescent proteins for multicolor in vivo imaging
Nature Methods 10, 751–754 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 source
- Wu, B. et. al., 2011 Modern fluorescent proteins and imaging technologies to study gene expression, nuclear localization, and dynamics
Curr Opin Cell Biol. 23(3): 310–317 source
- Goedhart, J. et. al., 2010 Bright cyan fluorescent protein variants identified by fluorescence lifetime screening
Nature Methods 7(2):137-9 source
- Shcherbo, D. et. al., 2009 Far-red fluorescent tags for protein imaging in living tissues.
Biochem J. 418(3):567-74 source
- Nienhaus, G.U. et. al., 2008: Optimized and Far-Red-Emitting Variants of Fluorescent Protein eqFP611.
Chem Biol. 15(3):224-33. source
- Shaner, N.C. et. al., 2007: Advances in fluorescent protein technology
J Cell Sci 120, 4247-4260. source
- Koushik, Srinagesh V. et. al. , 2006: Cerulean, Venus, and VenusY67C FRET Reference Standards
Biophys J. 91(12): L99–L101. source
- Eisenstein, Michael, 2006: Helping cells to tell a colorful tale
Nature Methods 3, 647 - 655 source
[edit] Techniques
- Becker, W., 2012: Fluorescence lifetime imaging – techniques and applications
J Microsc. 247(2):119-36 source
- Weber, M. et.al., 2011: Light sheet microscopy for real-time developmental biology
Curr Opin Genet Dev. 21(5):566-72 source
- Truong, T.V. et. al., 2011: Deep and fast live imaging with two-photon scanned light-sheet microscopy
Nature Methods 8, 757–760 source
- Min, W. et. al., 2011: Coherent nonlinear optical imaging: beyond fluorescence microscopy
Annu Rev Phys Chem. 62:507-30 source
- Hell, S.W., 2009: Microscopy and its focal switch
Nature Methods 6, 24 - 32 source
- Evans, C.L., et. al. 2008: Coherent Anti-Stokes Raman Scattering Microscopy: Chemical Imaging for Biology and Medicine
Annu Rev Anal Chem 1:883-909 source
- Mazza, D. et. al., 2008:A New FRAP/FRAPa Method For 3-D Diffusion Measurements Based On Multi-photon Excitation Microscopy
Biophys J. 95(7):3457-69 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. 32(14):2007-9 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 26 (11), 828-830 source
[edit] Technical Tests
- Cole, R.W. et. al., 2011: Measuring and interpreting point spread functions to determine confocal microscope resolution and ensure quality control
Nat Protoc. 6(12):1929-41 source
- 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
- Zucker, Robert M., 2001: Evaluation of confocal microscopy system performance.
Cytometry 44(4):273-94 source
[edit] Image Processing and Analysis
[edit] 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
[edit] 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)