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Volumn , Issue MARCH, 2011, Pages 2-

ESPINA: A tool for the automated segmentation and counting of synapses in large stacks of electron microscopy images

Author keywords

3D reconstruction; Focused ion beam; Quantification; Scanning electron microscopy; Segmentation; Software; Synapses

Indexed keywords

ACCURACY; ARTICLE; AUTOMATION; BRAIN COMPUTER INTERFACE; BRAIN TISSUE; CALIBRATION; DATA ANALYSIS SOFTWARE; ELECTRON MICROSCOPY; GABAERGIC SYSTEM; GABAERGIC TRANSMISSION; IMAGE ANALYSIS; IMAGE DISPLAY; IMAGE PROCESSING; IMAGE RECONSTRUCTION; LIMIT OF QUANTITATION; MENTAL TASK; NONHUMAN; SCANNING ELECTRON MICROSCOPY; SYNAPTIC INHIBITION; SYNAPTIC POTENTIAL; TASK PERFORMANCE; THREE DIMENSIONAL IMAGING; TISSUE SECTION;

EID: 84862983600     PISSN: 16625129     EISSN: None     Source Type: Journal    
DOI: 10.3389/fnana.2011.00018     Document Type: Article
Times cited : (60)

References (27)
  • 2
    • 54049127490 scopus 로고    scopus 로고
    • Ultrastructure of dendritic spines: Correlation between synaptic and spine morphologies
    • doi: 10.3389/ neuro.01/1.1.010.2007
    • Arellano, J. I., Benavides-Piccione, R., Defelipe, J., and Yuste, R. (2007). Ultrastructure of dendritic spines: correlation between synaptic and spine morphologies. Front. Neurosci. 1:131-143. doi: 10.3389/ neuro.01/1.1.010.2007
    • (2007) Front. Neurosci , vol.1 , pp. 131-143
    • Arellano, J.I.1    Benavides-Piccione, R.2    Defelipe, J.3    Yuste, R.4
  • 3
    • 36048945922 scopus 로고    scopus 로고
    • ImageJ for microscopy
    • Collins, T. J. (2007). ImageJ for microscopy. Biotechniques 43, 25-30.
    • (2007) Biotechniques , vol.43 , pp. 25-30
    • Collins, T.J.1
  • 4
    • 0014305851 scopus 로고
    • Synaptic patterns on different cell types in the different laminae of the cat visual cortex. An electron microscope study
    • Colonnier, M. (1968). Synaptic patterns on different cell types in the different laminae of the cat visual cortex. An electron microscope study. Brain Res. 9, 268-287.
    • (1968) Brain Res , vol.9 , pp. 268-287
    • Colonnier, M.1
  • 5
    • 0021940309 scopus 로고
    • An empirical assessment of stereological formulae applied to the counting of synaptic disks in the cerebral cortex
    • Colonnier, M., and Beaulieu, C. (1985). An empirical assessment of stereological formulae applied to the counting of synaptic disks in the cerebral cortex. J. Comp. Neurol. 231, 175-179.
    • (1985) J. Comp. Neurol , vol.231 , pp. 175-179
    • Colonnier, M.1    Beaulieu, C.2
  • 6
    • 0038372036 scopus 로고    scopus 로고
    • Microstructure of the neocortex: Comparative aspects
    • DeFelipe, J., Alonso-Nanclares, L., and Arellano, J. I. (2002). Microstructure of the neocortex: comparative aspects. J. Neurocytol. 31, 299-316.
    • (2002) J. Neurocytol , vol.31 , pp. 299-316
    • Defelipe, J.1    Alonso-Nanclares, L.2    Arellano, J.I.3
  • 7
    • 0032741181 scopus 로고    scopus 로고
    • Estimation of the number of synapses in the cerebral cortex: Methodological considerations
    • DeFelipe, J., Marco, P., Busturia, I., and Merchán-Pérez, A. (1999). Estimation of the number of synapses in the cerebral cortex: methodological considerations. Cereb. Cortex 9, 722-732.
    • (1999) Cereb. Cortex , vol.9 , pp. 722-732
    • Defelipe, J.1    Marco, P.2    Busturia, I.3    Merchán-Pérez, A.4
  • 8
    • 14044262855 scopus 로고    scopus 로고
    • Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure
    • doi: 10.1371/ journal.pbio.0020329
    • Denk, W., and Horstmann, H. (2004). Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure. PLoS Biol. 2, e329. doi: 10.1371/ journal.pbio.0020329
    • (2004) PLoS Biol , vol.2
    • Denk, W.1    Horstmann, H.2
  • 9
    • 17144363197 scopus 로고    scopus 로고
    • Reconstruct: A free editor for serial section microscopy
    • Fiala, J. C. (2005). Reconstruct: a free editor for serial section microscopy. J. Microsc. 218, 52-61.
    • (2005) J. Microsc , vol.218 , pp. 52-61
    • Fiala, J.C.1
  • 10
    • 70349202507 scopus 로고    scopus 로고
    • Visualization of multi-variate scientific data
    • Fuchs, R., and Hauser, H. (2009). Visualization of multi-variate scientific data. Comput. Graph. Forum 28, 1670-1690.
    • (2009) Comput. Graph. Forum , vol.28 , pp. 1670-1690
    • Fuchs, R.1    Hauser, H.2
  • 11
    • 0001186564 scopus 로고
    • Axo-somatic and axodendritic synapses of the cerebral cortex: An electron microscope study
    • Gray, E. G. (1959). Axo-somatic and axodendritic synapses of the cerebral cortex: an electron microscope study. J. Anat. 93, 420-433.
    • (1959) J. Anat , vol.93 , pp. 420-433
    • Gray, E.G.1
  • 13
    • 34347211797 scopus 로고    scopus 로고
    • Serial sectioning and electron microscopy of large tissue volumes for 3D analysis and reconstruction: A case study of the calyx of held
    • Hoffpauir, B. K., Pope, B. A., and Spirou, G. A. (2007). Serial sectioning and electron microscopy of large tissue volumes for 3D analysis and reconstruction: a case study of the calyx of held. Nat. Protoc. 2, 9-22.
    • (2007) Nat. Protoc , vol.2 , pp. 9-22
    • Hoffpauir, B.K.1    Pope, B.A.2    Spirou, G.A.3
  • 14
    • 0001797609 scopus 로고
    • GABA neurons in the cerebral cortex
    • Functional Properties of Cortical Cells, eds E. G. Jones and A. Peters (New York: Plenum Press
    • Houser, C. R., Vaughn, J. E., Hendry, S. H. C., Jones, E. G., and Peters, A. (1984). "GABA neurons in the cerebral cortex," in Cerebral Cortex, Vol. 2, Functional Properties of Cortical Cells, eds E. G. Jones and A. Peters (New York: Plenum Press), 63-89.
    • (1984) Cerebral Cortex , vol.2 , pp. 63-89
    • Houser, C.R.1    Vaughn, J.E.2    Hendry, S.H.C.3    Jones, E.G.4    Peters, A.5
  • 17
    • 41149120500 scopus 로고    scopus 로고
    • Serial section scanning electron microscopy of adult brain tissue using focused ion beam milling
    • Knott, G., Marchman, H., Wall, D., and Lich, B. (2008). Serial section scanning electron microscopy of adult brain tissue using focused ion beam milling. J. Neurosci. 28, 2959-2964.
    • (2008) J. Neurosci , vol.28 , pp. 2959-2964
    • Knott, G.1    Marchman, H.2    Wall, D.3    Lich, B.4
  • 18
    • 0029879295 scopus 로고    scopus 로고
    • Computer visualization of three-dimensional image data using IMOD
    • Kremer, J. R., Mastronarde, D. N., and McIntosh, J. R. (1996). Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116, 71-76.
    • (1996) J. Struct. Biol , vol.116 , pp. 71-76
    • Kremer, J.R.1    Mastronarde, D.N.2    McIntosh, J.R.3
  • 19
    • 84870908566 scopus 로고    scopus 로고
    • Label object representation and manipulation with ITK
    • Lehmann, G. (2008). Label object representation and manipulation with ITK. Insight J. 1-34.
    • (2008) Insight J , pp. 1-34
    • Lehmann, G.1
  • 20
    • 77954847643 scopus 로고    scopus 로고
    • Counting synapses using FIB/SEM microscopy: A true revolution for ultrastructural volume reconstruction
    • doi: 10.3389/neuro.05.018.2009
    • Merchán-Pérez, A., Rodriguez, J., AlonsoNanclares, L., Schertel, A., and Defelipe, J. (2009a). Counting synapses using FIB/SEM microscopy: a true revolution for ultrastructural volume reconstruction. Front. Neuroanat. 3:18. doi: 10.3389/neuro.05.018.2009
    • (2009) Front. Neuroanat , vol.3 , pp. 18
    • Merchán-Pérez, A.1    Rodriguez, J.2    Alonsonanclares, L.3    Schertel, A.4    Defelipe, J.5
  • 21
    • 67649861375 scopus 로고    scopus 로고
    • Proximity of excitatory and inhibitory axon terminals adjacent to pyramidal cell bodies provides a putative basis for nonsynaptic interactions
    • Merchán-Párez, A., Rodriguez, J., Ribak, C. E., and DeFelipe, J. (2009b). Proximity of excitatory and inhibitory axon terminals adjacent to pyramidal cell bodies provides a putative basis for nonsynaptic interactions. Proc. Natl. Acad. Sci. U.S.A. 106, 9878-9883.
    • (2009) Proc. Natl. Acad. Sci. U.S.A , vol.106 , pp. 9878-9883
    • Merchán-Peárez, A.1    Rodriguez, J.2    Ribak, C.E.3    Defelipe, J.4
  • 22
    • 0030480767 scopus 로고    scopus 로고
    • The morphology of synapses
    • Peters, A., and Palay, S. L. (1996). The morphology of synapses. J. Neurocytol. 25, 687-700.
    • (1996) J. Neurocytol , vol.25 , pp. 687-700
    • Peters, A.1    Palay, S.L.2
  • 24
    • 51549110953 scopus 로고    scopus 로고
    • A visualization and segmentation toolbox for electron microscopy
    • Pruggnaller, S., Mayr, M., and Frangakis, A. S. (2008). A visualization and segmentation toolbox for electron microscopy. J. Struct. Biol. 164, 161-165.
    • (2008) J. Struct. Biol , vol.164 , pp. 161-165
    • Pruggnaller, S.1    Mayr, M.2    Frangakis, A.S.3
  • 25
    • 0034228837 scopus 로고    scopus 로고
    • The SCRUM software development process for small teams
    • Rising, L., and Janoff, N. S. (2000). The SCRUM software development process for small teams. IEEE Softw. 17, 26-32.
    • (2000) IEEE Softw , vol.17 , pp. 26-32
    • Rising, L.1    Janoff, N.S.2
  • 26
    • 0021234096 scopus 로고
    • The unbiased estimation of number and sizes of arbitrary particles using the dissector
    • Sterio, D. C. (1984). The unbiased estimation of number and sizes of arbitrary particles using the dissector. J. Microsc. 134, 127-136.
    • (1984) J. Microsc , vol.134 , pp. 127-136
    • Sterio, D.C.1
  • 27
    • 0038104443 scopus 로고
    • Cortical Circuits: Synaptic Organization of the Cerebral Cortex
    • Boston: Birkhäuser
    • White, E. (1989). Cortical Circuits: Synaptic Organization of the Cerebral Cortex. Structure, Function, and Theory. Boston: Birkhäuser.
    • (1989) Structure, Function, and Theory
    • White, E.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.