External Resources

Cromey, DW
Avoiding Twisted Pixels: Ethical Guidelines for the Appropriate Use and Manipulation of Scientific Digital Images
Sci Eng Ethics. 2010 Dec;16(4):639-67

Pearson, H
The good, the bad and the ugly
Nature. 2007 May 10;447(7141):138-40

Brown, CM
Fluorescence microscopy - avoiding the pitfalls
J Cell Sci. 2007 May 15;120(Pt 10):1703-5

Eisenstein, Michael
Something to see
Nature. 2006 Oct 26;443(7114):1017-21

Pawley, J
The 39 Steps: A Cautionary Tale about “quantatative” 3D Fluorescence Microscopy
Biotechniques. 2000 May;28(5):884-6, 888

Becker, W
Fluorescence lifetime imaging – techniques and applications
J Microsc. 2012 Aug;247(2):119-36

Weber, M and Huisken J
Light sheet microscopy for real-time developmental biology
Curr Opin Genet Dev. 2011 Oct;21(5):566-72

Truong TV, Supatto W, Koos DS, Choi JM, Fraser SE
Deep and fast live imaging with two-photon scanned light-sheet microscopy
Nat Methods. 2011 Jul 17;8(9):757-60

Min W, Freudiger CW, Lu S, Xie XS
Coherent nonlinear optical imaging: beyond fluorescence microscopy
Annu Rev Phys Chem. 2011;62:507-30

Hell, SW
Microscopy and its focal switch
Nat Methods. 2009 Jan;6(1):24-32

Evans, CL and Xie XS
Coherent Anti-Stokes Raman Scattering Microscopy: Chemical Imaging for Biology and Medicine
Annu Rev Anal Chem. 2008;1:883-909

Mazza D, Braeckmans K, Cella F, Testa I, Vercauteren D, Demeester J, De Smedt SS, Diaspro A
A New FRAP/FRAPa Method For 3-D Diffusion Measurements Based On Multi-photon Excitation Microscopy
Biophys J. 2008 Oct;95(7):3457-69

Göbel W, Kampa BM, Helmchen F.
Imaging cellular network dynamics in three dimensions using fast 3D laser scanning
Nat Methods. 2007 Jan;4(1):73-9

Botcherby EJ, Juskaitis R, Booth MJ, Wilson T
Aberration-free optical refocusing in high numerical aperture microscopy
Opt Lett. 2007 Jul 15;32(14):2007-9

Donnert G, Eggeling C, Hell SW
Major signal increase in fluorescence microscopy through dark-state relaxation
Nat Methods. 2007 Jan;4(1):81-6

Frohn JT, Knapp HF, Stemmer A
Three-dimensional resolution enhancement in fluorescence microscopy by harmonic excitation
Opt Lett. 2001 Jun 1;26(11):828-30

Shcherbakova DM, Verkhusha VV
Near-infrared fluorescent proteins for multicolor in vivo imaging
Nat Methods. 2013 Aug;10(8):751-4

Shcherbakova DM, Subach OM, Verkhusha VV
Red fluorescent proteins: advanced imaging applications and future design
Angew Chem Int Ed Engl. 2012 Oct 22;51(43):10724-38

Wu B, Piatkevich KD, Lionnet T, Singer RH, Verkhusha VV
Modern fluorescent proteins and imaging technologies to study gene expression, nuclear localization, and dynamics
Curr Opin Cell Biol. 2011 Jun;23(3):310-7

Goedhart J, van Weeren L, Hink MA, Vischer NO, Jalink K, Gadella TW Jr
Bright cyan fluorescent protein variants identified by fluorescence lifetime screening
Nat Methods. 2010 Feb;7(2):137-9

Shcherbo D et al.
Far-red fluorescent tags for protein imaging in living tissues
Biochem J. 2009 Mar 15;418(3):567-74

Kredel S et al.
Optimized and Far-Red-Emitting Variants of Fluorescent Protein eqFP611
Chem Biol. 2008 Mar;15(3):224-33

Shaner NC, Patterson GH, Davidson MW
Advances in fluorescent protein technology
J Cell Sci. 2007 Dec 15;120(Pt 24):4247-60

Koushik SV, Chen H, Thaler C, Puhl HL 3rd, Vogel SS
Cerulean, Venus, and VenusY67C FRET Reference Standards
Biophys J. 2006 Dec 15;91(12):L99-L101

Eisenstein M
Helping cells to tell a colorful tale
Nat Methods. 2006 Aug; 3(8): 647 - 655

Cole, RW, Brown CM, Jinadasa T
Measuring and interpreting point spread functions to determine confocal microscope resolution and ensure quality control
Nat Protoc. 2011 Nov 10;6(12):1929-41

Murray, JM, Appleton PL, Swedlow JR, Waters JC
Evaluating performance in three-dimensional fluorescence microscopy
J Micros. 2007 Dec;228(Pt 3):390-405

Zucker, RM
Quality Assessment of Confocal Microscopy Slide Based Systems: Performance
Cytometry A. 2006 Jul;69(7):659-76

Zucker, RM
Quality Assessment of Confocal Microscopy Slide-Based Systems: Instability
Cytometry A. 2006 Jul;69(7):677-90

Zucker, RM
Reliability of confocal microscopy spectral imaging systems: Use of multispectral beads
Cytometry A. 2007 Mar;71(3):174-89

Zucker, RM, Price O
Evaluation of confocal microscopy system performance
Cytometry. 2001 Aug 1;44(4):273-94

Mitchel, JA, Martin, IS, Hoffman-Kim, D
Neurient: An algorithm for automatic tracing of confluent neuronal images to determine alignment
J Neurosci Methods. 2013 Apr 15;214(2):210-22

Meijering, E, Dzyubachyk, O, Smal, I
Methods for Cell and Particle Tracking
Methods Enzymol. 2012;504:183-200

Dima AA, Elliott JT, Filliben JJ, Halter M, Peskin A, Bernal J, Kociolek M, Brady MC, Tang HC, Plant AL
Comparison of segmentation algorithms for fluorescence microscopy images of cells
Cytometry A. 2011 Jul;79(7):545-59

Padmanabhan K, Eddy WF, Crowley JC
A novel algorithm for optimal image thresholding of biological data
J Neurosci Methods. 2010 Nov 30;193(2):380-4

Dunn KW, Kamocka MM, McDonald JH
A practical guide to evaluating colocalization in biological microscopy
Am J Physiol Cell Physiol. 2011 Apr;300(4):C723-42

Bolte S, Cordelières FP
A guided tour into subcellular colocalization analysis in light microscopy
J Microsc. 2006 Dec;224(Pt 3):213-32
(Good paper to start with if you want to learn more about colocalization. Covers all relevant points.)

Costes SV, Daelemans D, Cho EH, Dobbin Z, Pavlakis G, Lockett S
Automatic and Quantitative Measurement of Protein-Protein Colocalization in Live Cells
Biophys J. 2004 Jun;86(6):3993-4003

Manders, EMM, Verbeek FJ, Aten, JA
Measurement of co-localization of objects in dual-color confocal images
J Microscopy. 1993 March;169(Pt 3):375-382

Manders EMM, Stap J, Brakenhoff GJ, van Driel R, Aten JA
Dynamics of three-dimensional replication patterns during the S-phase, analyzed by double labelling of DNA and confocal microscopy
J Cell Sci. 1992 Nov;103(3):857-862