Deconvolution Microscopy Literature References
Deconvolution is a computational technique that is useful for improving the contrast and resolution of digital images gathered with fluorescence microscopy. The methodology includes numerous applications designed to remove or reverse the blurring present in microscopy images caused by the limited aperture of the microscope objective. Virtually any digital image captured with a widefield or confocal microscope can be improved by deconvolution, and new techniques that apply to transmitted light images are rapidly emerging. In particular, three-dimensional stacks are the ideal candidates for deconvolution.
Recommended Reading
- Agard, D. A. Optical Sectioning Microscopy: cellular architecture in three dimensions. Annual Review of Biophysics and Bioengineering 13: 191-219 (1984).
- Wallace, W., Schaefer, L. H. and Swedlow, J. R. A Workingperson's Guide to Deconvolution in Light Microscopy. BioTechniques 31: 1036-1097 (2001).
- Andrews. P.D., Harper, I. S. and Swedlow, J. R. To 5D and Beyond: Quantitative fluorescence microscopy in the postgenomic era. Traffic 3: 29-36 (2002).
- Swedlow, J. R. and Platani, M. Live cell imaging using wide-field microscopy and deconvolution. Cell Structure and Function 27: 335-341 (2002).
- Sibarita, J. B. Deconvolution microscopy. Advances in Biochemical Engineering and Biotechnology 95: 201-243 (2005).
- Murray, J. M., Appleton, P. L., Swedlow, J. R. and Waters, J. C. Evaluating performance in three dimensional fluorescence microscopy. Journal of Microscopy 228: 390-405 (2007).
- Swedlow, J. R., Hu, K., Andrews, P. d., Roos, D. S. and Murray, J. M. Measuring tubulin content in Toxoplasma gondii: a comparison of laser-scanning confocal and wide-field fluorescence microscopy. Proceedings of the National Academy of Sciences (USA) 99: 2014-2019 (2002).
- McNally, J. G., Karpova, T., Cooper, J. and Conchello, J. A. Three-dimensional imaging by deconvolution microscopy. Methods 19: 373-385 (1999).
- Carrington, W. A., Lynch, R. M., Moore, E. E. W., Isenberg, G., Fogarty, K. E. and Fay, F.S. Superresolution three-dimensional images of fluorescence in cells with minimal light exposure. Science 268: 1483-1487 (1995).
- Markham, J. and Conchello, J.A. Artefacts in restored images due to intensity loss in three-dimensional fluorescence microscopy. Journal of Microscopy 204: 93-98 (2001).
Additional Literature Sources
- Agard, D. A. and Sedat, J.W. Three-dimensional architecture of a polytene nucleus. Nature 302: 676-681 (1983).
- de Monvel, J. B., Scarfone, E., le Calvez, S. and Ulfendahl, M. Image-adaptive deconvolution for three-dimensional deep biological imaging. Biophysical Journal 85: 3991-4001 (2003).
- Dernburg, A. F., Broman, K. W., Fung, J. C., Marshall, W. F., Philips, J., Agard, D. A. and Sedat, J. W. Perturbation of nuclear architecture by long-distance chromosome interactions. Cell 85: 745-759 (1996).
- Egner, A. and Hell, S. W. Equivalence of the Huygens-Fresnel and Debye approach for the calculation of high aperture point-spread functions in the presence of refractive index mismatch. Journal of Microscopy 193: 244-249 (1999).
- Femino, A. M., Fay, F. S., Fogarty, K. and Singer, R. H. Visualization of single RNA transcripts in situ. Science 280: 585-590 (1998).
- Hanser, B. M., Gustafsson, M. G. L., Agard, D. A. and Sedat, J. W. Phase retrieval for high-numerical-aperture optical systems. Optics Letters 28: 801- 803 (2003).
- He, X., Asthana, S. and Sorger, P. K. Transient sister chromatid separation and elastic deformation of chromosomes during mitosis in budding yeast. Cell 101: 763-775 (2000).
- Hiraoka, Y., Sedat, J.W. and Agard, D. A. The use of a charge-coupled device for quantitative optical microscopy of biological structures. Science 238: 36-41 (1987).
- Hiraoka, Y., Sedat, J. W. and Agard, D. A. Determination of three-dimensional imaging properties of a light microscope system. Biophysical Journal 57: 325-333 (1990).
- Holmes, T. J. and O'Connor, N. J. Blind deconvolution of 3D transmitted light brightfield micrographs. Journal of Microscopy 200: 114-127 (2000).
- Kam, Z., Agard, D. A. and Sedat, J. W. Three-dimensional microscopy in thick biological samples: a fresh approach for adjusting focus and correcting spherical aberration. Bioimaging 5: 40-49 (1997).
- Kam, Z., Hanser, B., Gustafsson, M. G. L., Agard, D. A. and Sedat, J. W. Computational adaptive optics for live three-dimensional biological imaging. Proceedings of the National Academy of Sciences (USA) 98: 3790-3795 (2001).
- Kozubek, M., Matula, P., Matula, P. and Kozubek, S. Automated acquisition and processing of multidimensional image data in confocal in vivo microscopy. Microscopy Research and Technique 64: 164-175 (2004).
- Marian, A., Charriere, F., Colomb, T., Montfort, F., Kuhn, J., Marquet, P. and Depeursinge, C. On the complex three-dimensional amplitude point spread function of lenses and microscope objectives: theoretical aspects, simulations and measurements by digital holography. Journal of Microscopy 225: 156-169 (2007).
- Qian, H., Sheetz, M. P. and Elson, E. L. Single particle tracking. Analysis of diffusion and flow in two-dimensional systems. Biophysical Journal 60: 910-921 (1991).
- Rizzuto, R., Carrington, W. and Tuft, R. A. Digital imaging microscopy of living cells. Trends in Cell Biology 8: 288-292 (1998).
- Ronneberger, O., Baddeley, D., Scheipl, F., Verveer, P. J., Burkhardt, H., Cremer, C., Fahrmeir, L, Cremer, T. and Joffe, B. Spatial quantitative analysis of fluorescently labeled nuclear structures: problems, methods, pitfalls. Chromosome Research 16: 523-562 (2008).
- Sarder, P. and Nehorai, A. Deconvolution methods for 3-D fluorescence microscopy images. IEEE Signal Processing Magazine 23: 32-45 (2006).
- Scalettar, B. A., Swedlow, J. R., Sedat, J. W. and Agard, D. A. Dispersion, aberration and deconvolution in multi-wavelength fluorescence images. Journal of Microscopy 182: 50-60 (1996).
- Schaefer, B. C., Ware, M. F., Marrack, P., Fanger, G. R., Kappler, J. W., Johnson, G. L. and Monks, C. R. F. Live cell fluorescence imaging of T cell MEKK2: redistribution and activation in response to antigen stimulation of the T cell receptor. Immunity 11: 411-421 (1999).
- Schaefer, L. H., Schuster, D. and Herz, H. Generalized approach for accelerated maximum likelihood based image restoration applied to three-dimensional fluorescence microscopy. Journal of Microscopy 204: 99-107 (2001).
- Schlecht, J., Barnard, K. and Pryor, B. Statistical inference of biological structure and point spread functions in 3D microscopy. Third International Symposium on 3D Data Processing, Visualization and Transmission 1: 373-380 (2006).
- Sedarat, F., Lin, E., Moore, E. D. W. and Tibbits, G. F. Deconvolution of confocal images of dihydropyridine and ryanodine receptors in developing cardiomyocytes. Journal of Applied Physiology 97: 1098-1103 (2004).
- Swedlow, J.R., Sedat, J. W. and Agard, D. A. Multiple chromosomal populations of topoisomerase II detected in vivo by time-lapse, three-dimensional wide-field microscopy. Cell 73: 97-108 (1993).
- Von Tiedemann, M., Fridberger, A., Ulfendahl, M. and De Monvel, J. B. Image Adaptive point-spread function estimation and deconvolution for in vivo confocal microscopy. Microscopy Research and Technique 69: 10-20 (2006).
- Vermolen, B. J., Garini, Y. and Young, I. T. 3D restoration with multiple images acquired by a modified conventional microscope. Microscopy Research and Technique 64: 113-125 (2004).
- Verveer, P. J., Gemkow, M. J. and Jovin, T. M. A comparison of image restoration approaches applied to three-dimensional confocal and wide-field fluorescence microscopy. Journal of Microscopy 193: 50-61 (1999).
- Yoo, H., Song, I. and Gweon, D. G. Measurement and restoration of the point spread function of fluorescence confocal microscopy. Journal of Microscopy 221: 172-176 (2006).
