|
AutoQuant Bibliography
Agard, D. A. (1984). "Optical Sectioning Microscopy: Cellular Architecture in Three Dimensions." Annual Review of Biophysics and Bioengineering. 13 191-219.
Aikens, R. S., D. A. Agard and J. W. Sedat. (1989). "Solid-State Imagers for Microscopy." Methods in Cell Biology. 29 291-313.
Ayers, G. R. and J. C. Dainty. (1988). "Iterative Blind Deconvolution Method and Its Applications." Optics Letters. 13(7): 547-549.
Bertero, M., P. Boccacci, G. J. Brakenhoff, F. Malfanti and H. T. M. Van der Voort. (1990). "Three-Dimensional Image Restoration and Super-Resolution in Fluorescence Confocal Microscopy." Journal of Microscopy. 157(1): 3-20.
Carrington, W. A. (1990). "Image Restoration in 3D Microscopy with Limited Data." Bioimaging and Two-Dimensional Spectroscopy, Los Angeles, SPIE. 1205. 72-83.
Cohen, A. R., B. Roysam and J. N. Turner. (1994). "Automated Tracing and Volume Measurements of Neurons from 3-D Confocal Fluorescence Microscopy Data." Journal of Microscopy. 173(2): 103-114.
Conchello, J. and E. Hansen. (1990). "Enhanced 3-D Reconstruction From Confocal Scanning Microscope Images. 1: Deterministic and Maximum Likelihood Reconstructions." Applied Optics. 29(26): 3795-3804.
Cooper, J. A., S. Bhattacharyya, J. N. Turner and T. J. Holmes. (1993). "Three-Dimensional Transmitted Light Brightfield Imaging: Pragmatic Data Collection and Preprocessing Considerations." MSA Annual Meeting, Cincinnati, San Francisco Press. 51. 276-277.
Deitch, J. S., K. L. Smith, J. W. Swann and J. N. Turner. (1991). "Ultrastructural Investigation of Neurons Identified and Localized Using the Confocal Scanning Laser Microscope." Journal of Electron Microscopy Technique. 18 82-90.
Dempster, A. P., N. M. Laird and D. B. Rubin. (1977). "Maximum Likelihood from Incomplete Data via the EM Algorithm." Journal of the Royal Statistical Society B. 39 1-37.
Elangovan M, Wallrabe H, Chen Y, Day R, Barroso M, and Periasamy A. (2003). “Characterization of one- and two-photon excitation fluorescence resonance energy transfer microscopy. Methods 29. 58-73.
Erhardt, A., G. Zinser, D. Komitowski and J. Bille. (1985). "Reconstructing 3-D Light-Microscopic Images by Digital Image Processing." Applied Optics. 24(2): 194-200. Media Cybernetics, Inc. Manual & Tutorials January, 2009 Page 145
Fay, F. S., W. Carrington and K. E. Fogarty. (1989). "Three-Dimensional Molecular Distribution in Single Cells Analysed using the Digital Imaging Microscope." Journal of Microscopy. 153(2): 133-149.
Gerchberg, R. W. and W. O. Saxton. (1974). "Super-Resolution Through Error Energy Reduction." Optica Acta. 21 709-720.
Gibson, S. F. and F. Lanni. (1991). "Experimental Test of an Analytical Model of Aberration in an Oil-Immersion Objective Lens Used in Three-Dimensional Light Microscopy." Journal of the Optical Society of America A. 8(10): 1601-1613.
Gordon G, Berry G, Liang X, Levine B, and Herman B. (1998). “Quantitative fluorescence resonance energy transfer measurements using fluorescence microscopy.” Biophysical Journal 74, 2702-2713.
Grynkiewicz G, Poenie M, and Tsien RY. (1985). “A new generation of Ca2+ indicators with greatly improved fluorescent properties.” Journal of Biological Chemistry 260, 3440-3450.
Hebert, T., R. Leahy and M. Singh. (1988). "Fast MLE for SPECT Using an Intermediate Polar Representation and a Stopping Criterion." IEEE Transactions on Nuclear Science. 35(1): 615-619.
Hiraoka, Y., J. W. Sedat and D. A. Agard. (1987). "The Use of Charge-Coupled Device for Quantitative Optical Microscopy of Biological Structures." Science. 238 36-41.
Hiraoka, Y., J. W. Sedat and D. A. Agard. (1990). "Determination of Three-Dimensional Imaging Properties of a Light Microscope System: Partial Confocal Behavior in Epifluorescence Microscopy." Biophysics Journal. 57 325-333.
Holmes, T. J., Bhattacharyya, S., Cooper, J. A., Hanzel, D., Krishnamurthi, V., Lin,W., Roysam, B., Szarowski, D. H., Turner, J. T., “Light Microscopic Images Reconstructed by Maximum Likelihood Deconvolution,” Chapter 24 in The Handbook of Biological Confocal Microscopy, 2nd Edition, James Pawley, Editor, Plenum Press, New York, 1995.
Holmes, T. J. (1989). "Expectation-Maximization Restoration of Band-Limited, Truncated Point-Process Intensities with Application in Microscopy." Journal of the Optical Society of America A. 6(7): 1006-1014.
Holmes, T. J. (1992). "Blind Deconvolution of Quantum-Limited Incoherent Imagery." Journal of the Optical Society of America A. 9(7): 1052-1061.
Holmes, T. J. and Y. H. Liu. (1989). "Richardson-Lucy/Maximum Likelihood Image Restoration for Fluorescence Microscopy: Further Testing." Applied Optics. 28(22): 4930-4938.
Holmes, T. J. and Y. H. Liu. (1991). "Acceleration of Maximum-Likelihood Image-Restoration for Fluorescence Microscopy and Other Noncoherent Imagery." Journal of the Optical Society of America A. 8(6): 893-907. Media Cybernetics, Inc. Manual & Tutorials January, 2009 Page 146
Holmes, T. J., Y. H. Liu, D. Khosla and D. A. Agard. (1991). "Increased Depth-of-Field and Stereo Pairs of Fluorescence Micrographs Via Inverse Filtering and Maximum Likelihood Estimation." Journal of Microscopy. 164(3): 217-237.
Janesick, J. R., T. Elliott and S. Collins. (1987). "Scientific Charge-Coupled Devices." Optical Engineering. 26(8): 692-714.
Joshi, S. and M. I. Miller. (1993). "Maximum a Posteriori Estimation with Good's Roughness for Three-Dimensional Optical-Sectioning Microscopy." Journal of the Optical Society of America A. 10(5): 1078-1085.
Kasten, F. H. (1993). "Introduction to Fluorescent Probes: Properties, History and Applications." Fluorescent Probes for Biological Function of Living Cells: A Practical Guide. Academic Press, London. in press.
Kimura, S. and C. Munakata. (1990). "Dependence of 3-D Optical Transfer Functions on the Pinhole Radius in a Fluorescent Confocal Optical Microscope." Applied Optics. 29(20): 3007-3011.
Krishnamurthi, V., Y. Liu, T. J. Holmes, B. Roysam and J. N. Turner. (1992). "Blind Deconvolution of 2D and 3D Fluorescent Micrographs." Biomedical Image Processing III and Three-Dimensional Microscopy, San Jose, SPIE. 1660. 95-102.
Krishnamurthi, V., J. N. Turner, Y. Liu and T. J. Holmes. (1994). "Blind Deconvolution for Fluorescence Microscopy by Maximum Likelihood Estimation." Applied Optics. in review.
Lalush, D. S. and M. W. Tsui. (1992). "Simulation Evaluation of Gibbs Prior Distributions for Use in Maximum A Posteriori SPECT Reconstructions." IEEE Transactions on Medical Imaging. 11(2): 267-275.
Lange, K. (1990). "Convergence of EM Image Reconstruction Algorithms with Gibbs Smoothing." IEEE Transactions on Medical Imaging. 9(4): 439-446.
Llacer, J. and E. Veklerov. (1989). "Feasible Images and Practical Stopping Rules for Iterative Algorithms in Emission Tomography." IEEE Transactions on Medical Imaging. 8(2): 186-193. errata 9(1):112(1990).
Lucy, L. B. (1974). "An Iterative Technique for the Rectification of Observed Distributions." The Astronomical Journal. 79(6): 745-765.
Macias-Garza, F., K. R. Diller, A. C. Bovik, S. J. Aggarwal and J. K. Aggarwal. (1989). "Improvement in the Resolution of Three-Dimensional Data Sets Collected Using Optical Serial Sectioning." Journal of Microscopy. 153(2): 205-221.
Martin, L. C. and B. K. Johnson. (1931). Practical Microscopy. Blackie and Son, London. Media Cybernetics, Inc. Manual & Tutorials January, 2009 Page 147
Miller, M. I., and B. Roysam, "Bayesian Image Reconstruction for Emission Tomography Incorporating Good's Roughness Prior on Massively Parallel Processors," Proceedings of the National Academy of Sciences, Vol. 88, No. 8, pp. 3223-3227, April 1991.
Miller, M. I. and D. L. Snyder. (1987). "The Role of Likelihood and Entropy in Incomplete-Data Problems: Applications to Estimating Point-Process Intensities and Toeplitz Constrained Covariances." Proceedings of the IEEE. 75 892-907.
Oppenheim, A. V. and R. W. Schafer. (1975). Digital Signal Processing. Prentice-Hall, Englewood Cliffs, NJ.
Poenie, M. (1990). Alteration of intracellular Fura-2 fluorescence by viscosity: a simple correction. Cell Calcium 11(2-3), 85-91.
Politte, D. G. and D. L. Snyder. (1991). "Corrections for Accidental Coincidences and Attenuation in Maximum-Likelihood Image Reconstruction for Positron-Emission Tomography." IEEE Transactions on Medical Imaging. 10(1): 82-89.
Richardson, W. H. (1972). "Baysian-Based Iterative Method of Image Restoration." Journal of the Optical Society of America. 62(1): 55-59.
Roysam, B., H. Ancin, A. K. Bhattacharjya, A. Chisti, R. Seegal and J. N. Turner. (1994). "Algorithms for Automated Characterization of Cell Populations in Thick Specimens from 3-D Confocal Fluorescence Data." Journal of Microscopy. 173(2): 115-126.
Roysam, B., A. K. Bhattacharjya, C. Srinivas and J. N. Turner. (1992). "Unsupervised Noise Removal Algorithms for 3-D Confocal Fluorescence Microscopy." Micron and Microscopica Acta. 23(4): 447-461.
Shaw, P. J. and D. J. Rawlins. (1991). "Three-Dimensional Fluorescence Microscopy." Progress in Biophysics and Molecular Biology. 56 187-213.
Shepp, L. A. and Y. Vardi. (1982). "Maximum Likelihood Reconstruction for Emission Tomography." IEEE Transactions on Medical Imaging. 1(2): 113-121.
Sheppard, C. J. R. and M. Gu. (1994). "3D Imaging in Brightfield Reflection and Transmission Microscopes." 3D Image Processing in Microscopy, Munich, Society for 3D Imaging in Microscopy.
Snyder, D. L., A. M. Hammoud and R. L. White. (1993). "Image Recovery from Data Acquired with a Charge-Coupled-Device Camera." Journal of the Optical Society of America A. 10(5): 1014-1023.
Snyder, D. L., M. I. Miller, L. J. Thomas and D. G. Politte. (1987). "Noise and Edge Artifacts in Maximum-Likelihood Reconstructions for Emission Tomography." IEEE Transactions on Medical Imaging. 6(3): 228-238. Media Cybernetics, Inc. Manual & Tutorials January, 2009 Page 148
Streibl, N. (1984). "Depth Transfer by an Imaging System." Optica Acta. 31 1233-1241.
Turner, J. N., K. L. Szarowski, S. M., A. Marko, A. Leith and J. W. Swann. (1991). "Confocal Microscopy and Three-Dimensional Reconstruction of Electrophysiologically Identified Neurons in Thick Brain Slices." Journal of Electron Microscopy Technique. 18 11-23.
Van Trees, H. L. (1968). Detection, Estimation, and Modulation Theory. Wiley , New York.
Veklerov, E. and J. Llacer. (1987). "Stopping Rule for the MLE Algorithm Based on Statistical Hypothesis Testing." IEEE Transactions on Biomedical Imaging. 6(4): 313-319.
Visser, T. D., J. L. Oud and G. J. Brakenhoff. (1992). "Refractive Index and Axial Distance Measurements in 3-D Microscopy." Optik. 90(1): 17-19.
R.H. Webb and C.K. Dorey, "The Pixelated Image," Chapter 4 in The Handbook of Biological Confocal Microscopy, 2nd Edition, James Pawley, Editor, Plenum Press, New York, 1995.
Willis, B., J. N. Turner, D. N. Collins, B. Roysam and T. J. Holmes. (1993). "Developments in Three-Dimensional Stereo Brightfield Microscopy." Microscopy Research and Technique. 24 437-451.
Wilson, T. (1987). "The Size of Detector in Confocal Imaging Systems." Optics Letters. 12 227-229.
| top
|