메뉴 건너뛰기




Volumn 9, Issue 4, 2003, Pages 296-310

Automated three-dimensional tracing of neurons in confocal and brightfield images

Author keywords

3 D brightfield microscopy; 3 D skeletonization; Automated neuron tracing; Confocal microscopy; Deconvolution; Reconnection

Indexed keywords

ANIMAL; ARTICLE; CAT; CONFOCAL MICROSCOPY; CYTOLOGY; FLUORESCENCE MICROSCOPY; IMAGE PROCESSING; METHODOLOGY; NERVE CELL; THREE DIMENSIONAL IMAGING; ULTRASTRUCTURE;

EID: 0042739762     PISSN: 14319276     EISSN: None     Source Type: Journal    
DOI: 10.1017/S143192760303040X     Document Type: Article
Times cited : (70)

References (58)
  • 1
    • 0021119618 scopus 로고
    • Optical sectioning microscopy: Cellular architecture in three dimensions
    • AGARD, D.A. (1984). Optical sectioning microscopy: Cellular architecture in three dimensions. Annu Rev Biophys Bioeng 13, 191-219.
    • (1984) Annu Rev Biophys Bioeng , vol.13 , pp. 191-219
    • Agard, D.A.1
  • 7
    • 0032585839 scopus 로고    scopus 로고
    • Rapid automated tracing and feature extraction from live high-resolution retinal fundus images using direct exploratory algorithms
    • CAN, A., SHEN, H., TURNER, J.N., TANENBAUM, H.L. & ROYSAM, B. (1999). Rapid automated tracing and feature extraction from live high-resolution retinal fundus images using direct exploratory algorithms. IEEE Trans Info Technol Biomed 3, 125-138.
    • (1999) IEEE Trans Info Technol Biomed , vol.3 , pp. 125-138
    • Can, A.1    Shen, H.2    Turner, J.N.3    Tanenbaum, H.L.4    Roysam, B.5
  • 8
    • 0033231865 scopus 로고    scopus 로고
    • Dendrites of classes of hippocampal neurons differ in structural complexity and branching patterns
    • CANNON, R.C., WHEAL, H.V. & TURNER, D.A. (1999). Dendrites of classes of hippocampal neurons differ in structural complexity and branching patterns. J Comp Neurol 413, 619-633.
    • (1999) J Comp Neurol , vol.413 , pp. 619-633
    • Cannon, R.C.1    Wheal, H.V.2    Turner, D.A.3
  • 10
    • 0002519261 scopus 로고
    • Tutorial on practical confocal microscopy and use of the confocal test specimen
    • Pawley, J. (Ed.). New York: Plenum Press
    • CENTONZE, V. & PAWLEY, J. (1995). Tutorial on practical confocal microscopy and use of the confocal test specimen. In The Handbook of Biological Confocal Microscopy, Pawley, J. (Ed.), pp. 549-557. New York: Plenum Press.
    • (1995) The Handbook of Biological Confocal Microscopy , pp. 549-557
    • Centonze, V.1    Pawley, J.2
  • 11
    • 0032761087 scopus 로고    scopus 로고
    • Dendogram generation for neural shape analysis
    • CESAR, R.M., JR. & COSTA, L. DA F. (1999). Dendogram generation for neural shape analysis. J Neurosci Meth 93, 121-131.
    • (1999) J Neurosci Meth , vol.93 , pp. 121-131
    • Cesar R.M., Jr.1    Costa, L.Da.F.2
  • 12
    • 0024552702 scopus 로고
    • Cable properties of cats spinal motoneurons measured by combining voltage clamp, current clamp and intracellular staining
    • CLEMENTS, J.D. & REDMAN, S.J. (1989). Cable properties of cats spinal motoneurons measured by combining voltage clamp, current clamp and intracellular staining. J Physiol 409, 63-87.
    • (1989) J Physiol , vol.409 , pp. 63-87
    • Clements, J.D.1    Redman, S.J.2
  • 13
    • 0028289552 scopus 로고
    • Automated tracing and volume measurements of neurons from 3-D confocal fluorescence microscopy data
    • COHEN, A.R., ROYSAM, B. & TURNER, J.N. (1994). Automated tracing and volume measurements of neurons from 3-D confocal fluorescence microscopy data. J Microsc 173, 103-114.
    • (1994) J Microsc , vol.173 , pp. 103-114
    • Cohen, A.R.1    Roysam, B.2    Turner, J.N.3
  • 16
    • 0027705542 scopus 로고
    • Three dimensional transmitted brightfield imaging: Pragmatic data collection and preprocessing considerations
    • Bailey, G.W. & Reider, C.L. (Eds.). San Francisco: San Francisco Press
    • COOPER, J.A., BHATTACHARYYA, S., TURNER, J.N. & HOLMES, T.J. (1993). Three dimensional transmitted brightfield imaging: Pragmatic data collection and preprocessing considerations. In Proceedings of the 51st Annual Meeting, Microscopy Society of America, Bailey, G.W. & Reider, C.L. (Eds.). San Francisco: San Francisco Press.
    • (1993) Proceedings of the 51st Annual Meeting, Microscopy Society of America
    • Cooper, J.A.1    Bhattacharyya, S.2    Turner, J.N.3    Holmes, T.J.4
  • 17
    • 0023200815 scopus 로고
    • Membrane area and dendritic structure in type-I identified triceps surae alpha motoneurons
    • CULLHEIM, S., FLESHMAN, J.W., GLENN, L.L. & BURKE, R.E. (1987). Membrane area and dendritic structure in type-I identified triceps surae alpha motoneurons. J Comp Neurol 255, 68-81.
    • (1987) J Comp Neurol , vol.255 , pp. 68-81
    • Cullheim, S.1    Fleshman, J.W.2    Glenn, L.L.3    Burke, R.E.4
  • 18
    • 0024996713 scopus 로고
    • Confocal scanning laser microscopic images of hippocampal neurons intracellularly labeled with biocytin
    • DEITCH, J.S., SMITH, K.L., CHONG, L.L., SWANS, J.W. & TURNER, J.N. (1990a). Confocal scanning laser microscopic images of hippocampal neurons intracellularly labeled with biocytin. J Neurosci Methods 33, 61-76.
    • (1990) J Neurosci Methods , vol.33 , pp. 61-76
    • Deitch, J.S.1    Smith, K.L.2    Chong, L.L.3    Swans, J.W.4    Turner, J.N.5
  • 19
    • 0025608420 scopus 로고
    • Parameters affecting imaging of the HRP-DAB reaction product in the confocal scanning laser microscope
    • DEITCH, J.S., SMITH, K.L., SWANN, J.W. & TURNER, J.N. (1990b). Parameters affecting imaging of the HRP-DAB reaction product in the confocal scanning laser microscope. J Microsc 160, 265-278.
    • (1990) J Microsc , vol.160 , pp. 265-278
    • Deitch, J.S.1    Smith, K.L.2    Swann, J.W.3    Turner, J.N.4
  • 20
    • 0025831271 scopus 로고
    • Ultrastructural investigation of neurons identified and localized using the confocal scanning laser microscope
    • DEITCH, J.S., SMITH, K.L., SWANN, J.W. & TURNER, J.N. (1991). Ultrastructural investigation of neurons identified and localized using the confocal scanning laser microscope. J Electron Microsc Tech 18, 82-90.
    • (1991) J Electron Microsc Tech , vol.18 , pp. 82-90
    • Deitch, J.S.1    Smith, K.L.2    Swann, J.W.3    Turner, J.N.4
  • 21
    • 0002629270 scopus 로고
    • Maximum likelihood from incomplete data via the EM Algorithm
    • DEMPSTER, A.D., LAIRD, N.M. & RUBIN, D.R. (1977). Maximum likelihood from incomplete data via the EM Algorithm. J R Stat Soc B 39, 1-37.
    • (1977) J R Stat Soc B , vol.39 , pp. 1-37
    • Dempster, A.D.1    Laird, N.M.2    Rubin, D.R.3
  • 22
    • 0042306406 scopus 로고    scopus 로고
    • Automatic 3D-Graph construction of nerve cells from confocal microscope scans
    • Tech Univ. Berlin, Germany
    • DIMA, A., SCHOLZ, M. & OBERMAYER, K. (2001). Automatic 3D-Graph construction of nerve cells from confocal microscope scans. Tech Report, Tech Univ. Berlin, Germany, http://edocs.tuberlin.de/einzeldokument/index.html.
    • (2001) Tech Report
    • Dima, A.1    Scholz, M.2    Obermayer, K.3
  • 27
    • 38249020627 scopus 로고
    • A note on: Thinning of 3-D images using the safe point thinning algorithm
    • GONG, W. & BERTRAND, G. (1990). A note on: Thinning of 3-D images using the safe point thinning algorithm. Pattern Recognit Lett 11, 499-500.
    • (1990) Pattern Recognit Lett , vol.11 , pp. 499-500
    • Gong, W.1    Bertrand, G.2
  • 29
    • 0027503192 scopus 로고
    • Aberrations in confocal fluorescence microscopy induced by imsmatches in refractive index
    • HELL, S., REINER, G., CREMER, C. & STELZER, E.H.K. (1993). Aberrations in confocal fluorescence microscopy induced by imsmatches in refractive index. J Microsc 169, 391-405.
    • (1993) J Microsc , vol.169 , pp. 391-405
    • Hell, S.1    Reiner, G.2    Cremer, C.3    Stelzer, E.H.K.4
  • 30
    • 0032225521 scopus 로고    scopus 로고
    • Tracking on tree-like structures in 3-D confocal images
    • Proceedings of 3-D and Multidimensional Microscopy: Image Acquisition and Processing V, Katzir, Abraham (Ed.)
    • HERZOG, A., KRELL, G., MICHAELIS, B. & ZUSCHRATTER, W. (1998). Tracking on tree-like structures in 3-D confocal images. In Proceedings of 3-D and Multidimensional Microscopy: Image Acquisition and Processing V, Katzir, Abraham (Ed.), vol. 3261 of SPIE: Biomed. Optics, pp. 165-176.
    • (1998) SPIE: Biomed. Optics , vol.3261 , pp. 165-176
    • Herzog, A.1    Krell, G.2    Michaelis, B.3    Zuschratter, W.4
  • 31
    • 0000781777 scopus 로고
    • Maximum likelihood image restoration adapted for noncoherent optical imaging
    • HOLMES, T.J. (1988). Maximum likelihood image restoration adapted for noncoherent optical imaging. J Opt Soc Am A 5, 666-673.
    • (1988) J Opt Soc Am A , vol.5 , pp. 666-673
    • Holmes, T.J.1
  • 32
    • 0026887712 scopus 로고
    • Blind deconvolution of quantum-limited incoherent imagery
    • HOLMES, T.J. (1992). Blind deconvolution of quantum-limited incoherent imagery. J Opt Soc Am A 9, 1052-1061.
    • (1992) J Opt Soc Am A , vol.9 , pp. 1052-1061
    • Holmes, T.J.1
  • 34
    • 0013506310 scopus 로고
    • Richardson-Lucy/maximum likelihood image restoration for fluorescence microscopy: Further testing
    • HOLMES, T.J. & LIU, Y.H. (1989). Richardson-Lucy/maximum likelihood image restoration for fluorescence microscopy: Further testing. Applied Optics 38, 4930-4938.
    • (1989) Applied Optics , vol.38 , pp. 4930-4938
    • Holmes, T.J.1    Liu, Y.H.2
  • 35
    • 0001943161 scopus 로고
    • Foundations of confocal scanned imaging in light microscopy
    • Pawley, J. (Ed.). New York: Plenum Press
    • INOUE, S. (1995). Foundations of confocal scanned imaging in light microscopy. In Handbook of Biological Confocal Microscopy, Pawley, J. (Ed.), pp. 1-18. New York: Plenum Press.
    • (1995) Handbook of Biological Confocal Microscopy , pp. 1-18
    • Inoue, S.1
  • 36
    • 0010099720 scopus 로고
    • Automatic morphometric analysis of neural cells
    • KIM, J. & DUNCAN, G. (1988). Automatic morphometric analysis of neural cells. Machine Graph Vis 7, 693-709.
    • (1988) Machine Graph Vis , vol.7 , pp. 693-709
    • Kim, J.1    Duncan, G.2
  • 38
    • 0030106145 scopus 로고    scopus 로고
    • An algorithm for a 3D simplicity test
    • LATECKI, L. & MA, C.M. (1996). An algorithm for a 3D simplicity test. Comput Vis Image Underst 63, 388-393.
    • (1996) Comput Vis Image Underst , vol.63 , pp. 388-393
    • Latecki, L.1    Ma, C.M.2
  • 39
    • 0028550697 scopus 로고
    • Building skeleton models via 3-D medial surface/axis thinning algorithms
    • LEE, T.C. & KASHYAP, R.L. (1994). Building skeleton models via 3-D medial surface/axis thinning algorithms. Graph Models Image Process 56, 6462-478.
    • (1994) Graph Models Image Process , vol.56 , pp. 6462-6478
    • Lee, T.C.1    Kashyap, R.L.2
  • 41
    • 0028425191 scopus 로고
    • On topology preservation in 3D thinning
    • MA, C.M. (1994). On topology preservation in 3D thinning. CVGIP: Image Underst 59, 328-339.
    • (1994) CVGIP: Image Underst , vol.59 , pp. 328-339
    • Ma, C.M.1
  • 42
    • 0030195504 scopus 로고    scopus 로고
    • Connectivity preservation of 3D 6-subiteration thinning algorithms
    • MA, C.M. (1996). Connectivity preservation of 3D 6-subiteration thinning algorithms. CVGIP: Graph Models Image Process 58, 382-386.
    • (1996) CVGIP: Graph Models Image Process , vol.58 , pp. 382-386
    • Ma, C.M.1
  • 43
    • 0030284743 scopus 로고    scopus 로고
    • A fully parallel 3D thinning algorithm and its applications
    • MA, C.M. & SONKA, M. (1996). A fully parallel 3D thinning algorithm and its applications. Comput Vis Image Underst, 420-433.
    • (1996) Comput Vis Image Underst , pp. 420-433
    • Ma, C.M.1    Sonka, M.2
  • 44
    • 0026345288 scopus 로고
    • Baysian image reconstruction for emission tomography incorporating good's roughness prior on massively parallel processors
    • MILLER, M.I. & ROYSAM, B. (1991). Baysian image reconstruction for emission tomography incorporating good's roughness prior on massively parallel processors. Proc Natl Acad Sci USA 88, 3223-3227.
    • (1991) Proc Natl Acad Sci USA , vol.88 , pp. 3223-3227
    • Miller, M.I.1    Roysam, B.2
  • 45
    • 38249005859 scopus 로고
    • Thinning of 3-D images using the safe point thinning algorithm
    • MUKHERJEE, J., CHATTERJI, B.N. & DAS, P.P. (1989). Thinning of 3-D images using the safe point thinning algorithm. Pattern Recognit Let 10, 167-173.
    • (1989) Pattern Recognit Let , vol.10 , pp. 167-173
    • Mukherjee, J.1    Chatterji, B.N.2    Das, P.P.3
  • 47
    • 0028515976 scopus 로고
    • Detection of 3-D simple points for topology preserving transformations with application to thinning
    • SAHA, P.K. & CHAUDHURI, B.B. (1994). Detection of 3-D simple points for topology preserving transformations with application to thinning. IEEE Tran Pattern Anal Machine Intell 16, 1028-1032.
    • (1994) IEEE Tran Pattern Anal Machine Intell , vol.16 , pp. 1028-1032
    • Saha, P.K.1    Chaudhuri, B.B.2
  • 48
    • 0001798739 scopus 로고    scopus 로고
    • Boundary surface-shrinking - A continuous approach to 3d center line extraction
    • Niemann, H., Seidel, H.-P. & Girod, B. (Eds.). Köln, Germany: IEEE Signal Processing Society
    • SCHIRMACHER, H., ZÖCKLER, M., STALLING, D. & HEGE, H.C. (1998). Boundary surface-shrinking - A continuous approach to 3d center line extraction. In Proceedings of Image Multidimensional Digital Signal Processing '98, Niemann, H., Seidel, H.-P. & Girod, B. (Eds.), pp. 25-28. Köln, Germany: IEEE Signal Processing Society.
    • (1998) Proceedings of Image Multidimensional Digital Signal Processing '98 , pp. 25-28
    • Schirmacher, H.1    Zöckler, M.2    Stalling, D.3    Hege, H.C.4
  • 49
    • 0042306405 scopus 로고    scopus 로고
    • Automatic three dimensional reconstruction of neurons from confocal images
    • Elsner, N. & Kreutzberg, G.W. (Eds.). Stuttgart Germany: Georg Thieme Verl
    • SCHMITT, S., DIMA, A., SCHOLZ, M. & OBERMAYER, K. (2001). Automatic three dimensional reconstruction of neurons from confocal images. 28th Göttingen Neurobiology Conference, Elsner, N. & Kreutzberg, G.W. (Eds.), vol. 2, p. 1042. Stuttgart Germany: Georg Thieme Verl.
    • (2001) 28th Göttingen Neurobiology Conference , vol.2 , pp. 104
    • Schmitt, S.1    Dima, A.2    Scholz, M.3    Obermayer, K.4
  • 50
    • 0000580043 scopus 로고    scopus 로고
    • Correction schemes for geometrically exact 3D reconstructions of neurons from confocal images
    • SCHOLZ, M., BUCHER, D., PFLÜGER, H.J. & OBERMAYER, K. (1999). Correction schemes for geometrically exact 3D reconstructions of neurons from confocal images. Soc Neurosci Abstr 24, 1508.
    • (1999) Soc Neurosci Abstr , vol.24 , pp. 1508
    • Scholz, M.1    Bucher, D.2    Pflüger, H.J.3    Obermayer, K.4
  • 52
    • 0035263432 scopus 로고    scopus 로고
    • Optimal scheduling of tracing computations for real-time vascular landmark extraction from retinal fundus images
    • SHEN, H., ROYSAM, B., STEWART, C.V., TURNER, J.N. & TANENBAUM, H.L. (2001). Optimal scheduling of tracing computations for real-time vascular landmark extraction from retinal fundus images. IEEE Trans Info Technol Biomed 5, 77-91.
    • (2001) IEEE Trans Info Technol Biomed , vol.5 , pp. 77-91
    • Shen, H.1    Roysam, B.2    Stewart, C.V.3    Turner, J.N.4    Tanenbaum, H.L.5
  • 53
    • 0019676108 scopus 로고
    • A parallel thinning algorithm for 3-D pictures
    • TSAO, Y.F. & FU, K.S. (1981). A parallel thinning algorithm for 3-D pictures. Comput Graph Image Process 17, 315-331.
    • (1981) Comput Graph Image Process , vol.17 , pp. 315-331
    • Tsao, Y.F.1    Fu, K.S.2
  • 55
    • 0019788228 scopus 로고
    • A quantitative light microscopic study of the dendrites of cat spinal-motoneurons after intracellular staining with horseradish peroxidase
    • ULFHAKE, B. & CULLHEIM, S. (1981). A quantitative light microscopic study of the dendrites of cat spinal-motoneurons after intracellular staining with horseradish peroxidase. J Comp Neurol 202, 585-596.
    • (1981) J Comp Neurol , vol.202 , pp. 585-596
    • Ulfhake, B.1    Cullheim, S.2
  • 56
    • 0021253647 scopus 로고
    • Electrophysiological and morphological measurements in cat gastroenemius and soleusmotoneurons
    • ULFHAKE, B. & KELLERTH, J.O. (1984). Electrophysiological and morphological measurements in cat gastroenemius and soleusmotoneurons. Brain Res 307, 167-179.
    • (1984) Brain Res , vol.307 , pp. 167-179
    • Ulfhake, B.1    Kellerth, J.O.2
  • 57
    • 0032224709 scopus 로고    scopus 로고
    • Extracting generalized cylinder models of dendritic trees from 3-D image stacks
    • Proceedings of 3-D and Multidimensional Microscopy: Image Acquisition and Processing V, Katzir, Abraham (Ed.)
    • XU, F., LEWIS, P.H., CHAD, J.E. & WHEAL, H.V. (1998). Extracting generalized cylinder models of dendritic trees from 3-D image stacks. In Proceedings of 3-D and Multidimensional Microscopy: Image Acquisition and Processing V, Katzir, Abraham (Ed.), vol. 3261 of SPIE: Biomed. Optics, pp. 149-158.
    • (1998) SPIE: Biomed. Optics , vol.3261 , pp. 149-158
    • Xu, F.1    Lewis, P.H.2    Chad, J.E.3    Wheal, H.V.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.