DOI: 10.1007/978-3-642-17274-8_32. Electron Microscopy Image Segmentation with Graph Cuts Utilizing Estimated Symmetric Three-Dimensional Shape Prior

Electron Microscopy Image Segmentation with Graph Cuts Utilizing Estimated Symmetric Three-Dimensional Shape Prior

10.1007/978-3-642-17274-8_32

Crossref book-chapter

Springer Berlin Heidelberg

Lecture Notes in Computer Science (297)

Bibliography

Yang, H.-F., & Choe, Y. (2010). Electron Microscopy Image Segmentation with Graph Cuts Utilizing Estimated Symmetric Three-Dimensional Shape Prior. Advances in Visual Computing, 322â331.

Authors 2

Huei-Fang Yang (first)
Yoonsuck Choe (additional)

References 20 Referenced 2

Helmstaedter, M., Briggman, K.L., Denk, W.: 3D structural imaging of the brain with photons and electrons. Current Opinion in Neurobiology 18, 633–641 (2008) (10.1016/j.conb.2009.03.005) / Current Opinion in Neurobiology by M. Helmstaedter (2008)
Briggman, K.L., Denk, W.: Towards neural circuit reconstruction with volume electron microscopy techniques. Current Opinion in Neurobiology 16, 562–570 (2006) (10.1016/j.conb.2006.08.010) / Current Opinion in Neurobiology by K.L. Briggman (2006)
Denk, W., Horstmann, H.: Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure. PLoS Biology 2, e329 (2004) (10.1371/journal.pbio.0020329)
Jain, V., Murray, J.F., Roth, F., Turaga, S., Zhigulin, V.P., Briggman, K.L., Helmstaedter, M., Denk, W., Seung, H.S.: Supervised learning of image restoration with convolutional networks. In: Proc. IEEE Int’l Conf. on Computer Vision, pp. 1–8 (2007) (10.1109/ICCV.2007.4408909)
Andres, B., Köthe, U., Helmstaedter, M., Denk, W., Hamprecht, F.A.: Segmentation of sbfsem volume data of neural tissue by hierarchical classification. In: Rigoll, G. (ed.) DAGM 2008. LNCS, vol. 5096, pp. 142–152. Springer, Heidelberg (2008) (10.1007/978-3-540-69321-5_15) / Pattern Recognition / Lecture Notes in Computer Science by B. Andres (2008)
Macke, J.H., Maack, N., Gupta, R., Denk, W., Schölkopf, B., Borst, A.: Contour-propagation algorithms for semi-automated reconstruction of neural processes. J. Neuroscience Methods 167, 349–357 (2008) (10.1016/j.jneumeth.2007.07.021) / J. Neuroscience Methods by J.H. Macke (2008)
Jurrus, E., Hardy, M., Tasdizen, T., Fletcher, P., Koshevoy, P., Chien, C.B., Denk, W., Whitaker, R.: Axon tracking in serial block-face scanning electron microscopy. Medical Image Analysis 13, 180–188 (2009) (10.1016/j.media.2008.05.002) / Medical Image Analysis by E. Jurrus (2009)
Li, S.Z.: Markov random field modeling in image analysis. Springer, New York (2001) (10.1007/978-4-431-67044-5) / Markov random field modeling in image analysis by S.Z. Li (2001)
Hammersley, J.M., Clifford, P.: Markov field on finite graphs and lattices (1971)
Kolmogorov, V., Zabih, R.: What energy functions can be minimized via graph cuts? IEEE Trans. Pattern Anal. Mach. Intell. 26, 147–159 (2004) (10.1109/TPAMI.2004.1262177) / IEEE Trans. Pattern Anal. Mach. Intell. by V. Kolmogorov (2004)
Boykov, Y., Veksler, O., Zabih, R.: Fast approximate energy minimization via graph cuts. IEEE Trans. Pattern Anal. Mach. Intell. 23, 1222–1239 (2001) (10.1109/34.969114) / IEEE Trans. Pattern Anal. Mach. Intell. by Y. Boykov (2001)
Bouix, S., Siddiqi, K., Tannenbaum, A.: Flux driven automatic centerline extraction. Medical Image Analysis 9, 209–221 (2005) (10.1016/j.media.2004.06.026) / Medical Image Analysis by S. Bouix (2005)
Hassouna, M.S., Farag, A.A.: Variational curve skeletons using gradient vector flow. IEEE Trans. Pattern Anal. Mach. Intell. 31, 2257–2274 (2009) (10.1109/TPAMI.2008.271) / IEEE Trans. Pattern Anal. Mach. Intell. by M.S. Hassouna (2009)
Gorelick, L., Galun, M., Sharon, E., Basri, R., Brandt, A.: Shape representation and classification using the poisson equation. IEEE Trans. Pattern Anal. Mach. Intell. 28, 1991–2005 (2006) (10.1109/TPAMI.2006.253) / IEEE Trans. Pattern Anal. Mach. Intell. by L. Gorelick (2006)
Vasilevskiy, A., Siddiqi, K.: Flux maximizing geometric flows. IEEE Trans. Pattern Anal. Mach. Intell. 24, 1565–1578 (2002) (10.1109/TPAMI.2002.1114849) / IEEE Trans. Pattern Anal. Mach. Intell. by A. Vasilevskiy (2002)
Kolmogorov, V., Boykov, Y.: What metrics can be approximated by geo-cuts, or global optimization of length/area and flux. In: Proc. IEEE Int’l Conf. Computer Vision, pp. 564–571 (2005) (10.1109/ICCV.2005.252)
Vu, N., Manjunath, B.S.: Graph cut segmentation of neuronal structures from transmission electron micrographs. In: Proc. Int’l Conf. Image Processing, pp. 725–728 (2008) (10.1109/ICIP.2008.4711857)
Boykov, Y., Funka-Lea, G.: Graph cuts and efficient N-D image segmentation. Int’l J. Computer Vision 70, 109–131 (2006) (10.1007/s11263-006-7934-5) / Int’l J. Computer Vision by Y. Boykov (2006)
Dice, L.R.: Measures of the amount of ecologic association between species. Ecology 26, 297–302 (1945) (10.2307/1932409) / Ecology by L.R. Dice (1945)
Cardona, A., Saalfeld, S., Tomancak, P., Hartenstein, V.: TrakEM2: open source software for neuronal reconstruction from large serial section microscopy data. In: Proc. High Resolution Circuits Reconstruction, pp. 20–22 (2009)

Dates

Type	When
Created	14 years, 9 months ago (Nov. 18, 2010, 11:09 p.m.)
Deposited	6 months, 1 week ago (Feb. 27, 2025, 9:14 p.m.)
Indexed	6 months, 1 week ago (Feb. 28, 2025, 12:38 a.m.)
Issued	15 years, 8 months ago (Jan. 1, 2010)
Published	15 years, 8 months ago (Jan. 1, 2010)
Published Print	15 years, 8 months ago (Jan. 1, 2010)

Funders 0

None

BibTeX

@inbook{Yang_2010, title={Electron Microscopy Image Segmentation with Graph Cuts Utilizing Estimated Symmetric Three-Dimensional Shape Prior}, ISBN={9783642172748}, ISSN={1611-3349}, url={http://dx.doi.org/10.1007/978-3-642-17274-8_32}, DOI={10.1007/978-3-642-17274-8_32}, booktitle={Advances in Visual Computing}, publisher={Springer Berlin Heidelberg}, author={Yang, Huei-Fang and Choe, Yoonsuck}, year={2010}, pages={322–331} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        2,
        28
      ]
    ],
    "date-time": "2025-02-28T05:38:03Z",
    "timestamp": 1740721083309,
    "version": "3.38.0"
  },
  "publisher-location": "Berlin, Heidelberg",
  "reference-count": 20,
  "publisher": "Springer Berlin Heidelberg",
  "isbn-type": [
    {
      "type": "print",
      "value": "9783642172731"
    },
    {
      "type": "electronic",
      "value": "9783642172748"
    }
  ],
  "license": [
    {
      "start": {
        "date-parts": [
          [
            2010,
            1,
            1
          ]
        ],
        "date-time": "2010-01-01T00:00:00Z",
        "timestamp": 1262304000000
      },
      "content-version": "unspecified",
      "delay-in-days": 0,
      "URL": "http://www.springer.com/tdm"
    }
  ],
  "content-domain": {
    "domain": [],
    "crossmark-restriction": false
  },
  "published-print": {
    "date-parts": [
      [
        2010
      ]
    ]
  },
  "DOI": "10.1007/978-3-642-17274-8_32",
  "type": "book-chapter",
  "created": {
    "date-parts": [
      [
        2010,
        11,
        19
      ]
    ],
    "date-time": "2010-11-19T04:09:27Z",
    "timestamp": 1290139767000
  },
  "page": "322-331",
  "source": "Crossref",
  "is-referenced-by-count": 2,
  "title": "Electron Microscopy Image Segmentation with Graph Cuts Utilizing Estimated Symmetric Three-Dimensional Shape Prior",
  "prefix": "10.1007",
  "author": [
    {
      "given": "Huei-Fang",
      "family": "Yang",
      "sequence": "first",
      "affiliation": []
    },
    {
      "given": "Yoonsuck",
      "family": "Choe",
      "sequence": "additional",
      "affiliation": []
    }
  ],
  "member": "297",
  "reference": [
    {
      "key": "32_CR1",
      "doi-asserted-by": "publisher",
      "first-page": "633",
      "DOI": "10.1016/j.conb.2009.03.005",
      "volume": "18",
      "author": "M. Helmstaedter",
      "year": "2008",
      "unstructured": "Helmstaedter, M., Briggman, K.L., Denk, W.: 3D structural imaging of the brain with photons and electrons. Current Opinion in Neurobiology\u00a018, 633\u2013641 (2008)",
      "journal-title": "Current Opinion in Neurobiology"
    },
    {
      "key": "32_CR2",
      "doi-asserted-by": "publisher",
      "first-page": "562",
      "DOI": "10.1016/j.conb.2006.08.010",
      "volume": "16",
      "author": "K.L. Briggman",
      "year": "2006",
      "unstructured": "Briggman, K.L., Denk, W.: Towards neural circuit reconstruction with volume electron microscopy techniques. Current Opinion in Neurobiology\u00a016, 562\u2013570 (2006)",
      "journal-title": "Current Opinion in Neurobiology"
    },
    {
      "key": "32_CR3",
      "doi-asserted-by": "crossref",
      "unstructured": "Denk, W., Horstmann, H.: Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure. PLoS Biology 2, e329 (2004)",
      "DOI": "10.1371/journal.pbio.0020329"
    },
    {
      "key": "32_CR4",
      "doi-asserted-by": "crossref",
      "unstructured": "Jain, V., Murray, J.F., Roth, F., Turaga, S., Zhigulin, V.P., Briggman, K.L., Helmstaedter, M., Denk, W., Seung, H.S.: Supervised learning of image restoration with convolutional networks. In: Proc. IEEE Int\u2019l Conf. on Computer Vision, pp. 1\u20138 (2007)",
      "DOI": "10.1109/ICCV.2007.4408909"
    },
    {
      "key": "32_CR5",
      "series-title": "Lecture Notes in Computer Science",
      "doi-asserted-by": "publisher",
      "first-page": "142",
      "DOI": "10.1007/978-3-540-69321-5_15",
      "volume-title": "Pattern Recognition",
      "author": "B. Andres",
      "year": "2008",
      "unstructured": "Andres, B., K\u00f6the, U., Helmstaedter, M., Denk, W., Hamprecht, F.A.: Segmentation of sbfsem volume data of neural tissue by hierarchical classification. In: Rigoll, G. (ed.) DAGM 2008. LNCS, vol.\u00a05096, pp. 142\u2013152. Springer, Heidelberg (2008)"
    },
    {
      "key": "32_CR6",
      "doi-asserted-by": "publisher",
      "first-page": "349",
      "DOI": "10.1016/j.jneumeth.2007.07.021",
      "volume": "167",
      "author": "J.H. Macke",
      "year": "2008",
      "unstructured": "Macke, J.H., Maack, N., Gupta, R., Denk, W., Sch\u00f6lkopf, B., Borst, A.: Contour-propagation algorithms for semi-automated reconstruction of neural processes. J. Neuroscience Methods\u00a0167, 349\u2013357 (2008)",
      "journal-title": "J. Neuroscience Methods"
    },
    {
      "key": "32_CR7",
      "doi-asserted-by": "publisher",
      "first-page": "180",
      "DOI": "10.1016/j.media.2008.05.002",
      "volume": "13",
      "author": "E. Jurrus",
      "year": "2009",
      "unstructured": "Jurrus, E., Hardy, M., Tasdizen, T., Fletcher, P., Koshevoy, P., Chien, C.B., Denk, W., Whitaker, R.: Axon tracking in serial block-face scanning electron microscopy. Medical Image Analysis\u00a013, 180\u2013188 (2009)",
      "journal-title": "Medical Image Analysis"
    },
    {
      "key": "32_CR8",
      "doi-asserted-by": "publisher",
      "DOI": "10.1007/978-4-431-67044-5",
      "volume-title": "Markov random field modeling in image analysis",
      "author": "S.Z. Li",
      "year": "2001",
      "unstructured": "Li, S.Z.: Markov random field modeling in image analysis. Springer, New York (2001)"
    },
    {
      "key": "32_CR9",
      "unstructured": "Hammersley, J.M., Clifford, P.: Markov field on finite graphs and lattices (1971)"
    },
    {
      "key": "32_CR10",
      "doi-asserted-by": "publisher",
      "first-page": "147",
      "DOI": "10.1109/TPAMI.2004.1262177",
      "volume": "26",
      "author": "V. Kolmogorov",
      "year": "2004",
      "unstructured": "Kolmogorov, V., Zabih, R.: What energy functions can be minimized via graph cuts? IEEE Trans. Pattern Anal. Mach. Intell.\u00a026, 147\u2013159 (2004)",
      "journal-title": "IEEE Trans. Pattern Anal. Mach. Intell."
    },
    {
      "key": "32_CR11",
      "doi-asserted-by": "publisher",
      "first-page": "1222",
      "DOI": "10.1109/34.969114",
      "volume": "23",
      "author": "Y. Boykov",
      "year": "2001",
      "unstructured": "Boykov, Y., Veksler, O., Zabih, R.: Fast approximate energy minimization via graph cuts. IEEE Trans. Pattern Anal. Mach. Intell.\u00a023, 1222\u20131239 (2001)",
      "journal-title": "IEEE Trans. Pattern Anal. Mach. Intell."
    },
    {
      "key": "32_CR12",
      "doi-asserted-by": "publisher",
      "first-page": "209",
      "DOI": "10.1016/j.media.2004.06.026",
      "volume": "9",
      "author": "S. Bouix",
      "year": "2005",
      "unstructured": "Bouix, S., Siddiqi, K., Tannenbaum, A.: Flux driven automatic centerline extraction. Medical Image Analysis\u00a09, 209\u2013221 (2005)",
      "journal-title": "Medical Image Analysis"
    },
    {
      "key": "32_CR13",
      "doi-asserted-by": "publisher",
      "first-page": "2257",
      "DOI": "10.1109/TPAMI.2008.271",
      "volume": "31",
      "author": "M.S. Hassouna",
      "year": "2009",
      "unstructured": "Hassouna, M.S., Farag, A.A.: Variational curve skeletons using gradient vector flow. IEEE Trans. Pattern Anal. Mach. Intell.\u00a031, 2257\u20132274 (2009)",
      "journal-title": "IEEE Trans. Pattern Anal. Mach. Intell."
    },
    {
      "key": "32_CR14",
      "doi-asserted-by": "publisher",
      "first-page": "1991",
      "DOI": "10.1109/TPAMI.2006.253",
      "volume": "28",
      "author": "L. Gorelick",
      "year": "2006",
      "unstructured": "Gorelick, L., Galun, M., Sharon, E., Basri, R., Brandt, A.: Shape representation and classification using the poisson equation. IEEE Trans. Pattern Anal. Mach. Intell.\u00a028, 1991\u20132005 (2006)",
      "journal-title": "IEEE Trans. Pattern Anal. Mach. Intell."
    },
    {
      "key": "32_CR15",
      "doi-asserted-by": "publisher",
      "first-page": "1565",
      "DOI": "10.1109/TPAMI.2002.1114849",
      "volume": "24",
      "author": "A. Vasilevskiy",
      "year": "2002",
      "unstructured": "Vasilevskiy, A., Siddiqi, K.: Flux maximizing geometric flows. IEEE Trans. Pattern Anal. Mach. Intell.\u00a024, 1565\u20131578 (2002)",
      "journal-title": "IEEE Trans. Pattern Anal. Mach. Intell."
    },
    {
      "key": "32_CR16",
      "doi-asserted-by": "crossref",
      "unstructured": "Kolmogorov, V., Boykov, Y.: What metrics can be approximated by geo-cuts, or global optimization of length/area and flux. In: Proc. IEEE Int\u2019l Conf. Computer Vision, pp. 564\u2013571 (2005)",
      "DOI": "10.1109/ICCV.2005.252"
    },
    {
      "key": "32_CR17",
      "doi-asserted-by": "crossref",
      "unstructured": "Vu, N., Manjunath, B.S.: Graph cut segmentation of neuronal structures from transmission electron micrographs. In: Proc. Int\u2019l Conf. Image Processing, pp. 725\u2013728 (2008)",
      "DOI": "10.1109/ICIP.2008.4711857"
    },
    {
      "key": "32_CR18",
      "doi-asserted-by": "publisher",
      "first-page": "109",
      "DOI": "10.1007/s11263-006-7934-5",
      "volume": "70",
      "author": "Y. Boykov",
      "year": "2006",
      "unstructured": "Boykov, Y., Funka-Lea, G.: Graph cuts and efficient N-D image segmentation. Int\u2019l J. Computer Vision\u00a070, 109\u2013131 (2006)",
      "journal-title": "Int\u2019l J. Computer Vision"
    },
    {
      "key": "32_CR19",
      "doi-asserted-by": "publisher",
      "first-page": "297",
      "DOI": "10.2307/1932409",
      "volume": "26",
      "author": "L.R. Dice",
      "year": "1945",
      "unstructured": "Dice, L.R.: Measures of the amount of ecologic association between species. Ecology\u00a026, 297\u2013302 (1945)",
      "journal-title": "Ecology"
    },
    {
      "key": "32_CR20",
      "unstructured": "Cardona, A., Saalfeld, S., Tomancak, P., Hartenstein, V.: TrakEM2: open source software for neuronal reconstruction from large serial section microscopy data. In: Proc. High Resolution Circuits Reconstruction, pp. 20\u201322 (2009)"
    }
  ],
  "container-title": "Lecture Notes in Computer Science",
  "original-title": [],
  "link": [
    {
      "URL": "http://link.springer.com/content/pdf/10.1007/978-3-642-17274-8_32",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "similarity-checking"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2025,
        2,
        28
      ]
    ],
    "date-time": "2025-02-28T02:14:16Z",
    "timestamp": 1740708856000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "http://link.springer.com/10.1007/978-3-642-17274-8_32"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2010
      ]
    ]
  },
  "ISBN": [
    "9783642172731",
    "9783642172748"
  ],
  "references-count": 20,
  "URL": "http://dx.doi.org/10.1007/978-3-642-17274-8_32",
  "relation": {},
  "ISSN": [
    "0302-9743",
    "1611-3349"
  ],
  "subject": [],
  "published": {
    "date-parts": [
      [
        2010
      ]
    ]
  }
}