Geometrical consistent 3D tracing of neuronal processes in ssTEM data

Verena Kaynig; Thomas J. Fuchs; Joachim M. Buhmann

doi:10.1007/978-3-642-15745-5_26

Geometrical consistent 3D tracing of neuronal processes in ssTEM data

Verena Kaynig
, Thomas J. Fuchs
, Joachim M. Buhmann

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

27 Scopus citations

Abstract

In neuroanatomy, automatic geometry extraction of neurons from electron microscopy images is becoming one of the main limiting factors in getting new insights into the functional structure of the brain. We propose a novel framework for tracing neuronal processes over serial sections for 3d reconstructions. The automatic processing pipeline combines the probabilistic output of a random forest classifier with geometrical consistency constraints which take the geometry of whole sections into account. Our experiments demonstrate significant improvement over grouping by Euclidean distance, reducing the split and merge error per object by a factor of two.

Original language	English
Title of host publication	Medical Image Computing and Computer-Assisted Intervention, MICCAI2010 - 13th International Conference, Proceedings
Pages	209-216
Number of pages	8
Edition	PART 2
DOIs	https://doi.org/10.1007/978-3-642-15745-5_26
State	Published - 2010
Externally published	Yes
Event	13th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2010 - Beijing, China Duration: 20 Sep 2010 → 24 Sep 2010

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Number	PART 2
Volume	6362 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	13th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2010
Country/Territory	China
City	Beijing
Period	20/09/10 → 24/09/10

Access to Document

10.1007/978-3-642-15745-5_26

Cite this

Kaynig, V., Fuchs, T. J., & Buhmann, J. M. (2010). Geometrical consistent 3D tracing of neuronal processes in ssTEM data. In Medical Image Computing and Computer-Assisted Intervention, MICCAI2010 - 13th International Conference, Proceedings (PART 2 ed., pp. 209-216). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6362 LNCS, No. PART 2). https://doi.org/10.1007/978-3-642-15745-5_26

Kaynig, Verena ; Fuchs, Thomas J. ; Buhmann, Joachim M. / Geometrical consistent 3D tracing of neuronal processes in ssTEM data. Medical Image Computing and Computer-Assisted Intervention, MICCAI2010 - 13th International Conference, Proceedings. PART 2. ed. 2010. pp. 209-216 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); PART 2).

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title = "Geometrical consistent 3D tracing of neuronal processes in ssTEM data",

abstract = "In neuroanatomy, automatic geometry extraction of neurons from electron microscopy images is becoming one of the main limiting factors in getting new insights into the functional structure of the brain. We propose a novel framework for tracing neuronal processes over serial sections for 3d reconstructions. The automatic processing pipeline combines the probabilistic output of a random forest classifier with geometrical consistency constraints which take the geometry of whole sections into account. Our experiments demonstrate significant improvement over grouping by Euclidean distance, reducing the split and merge error per object by a factor of two.",

author = "Verena Kaynig and Fuchs, \{Thomas J.\} and Buhmann, \{Joachim M.\}",

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doi = "10.1007/978-3-642-15745-5\_26",

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booktitle = "Medical Image Computing and Computer-Assisted Intervention, MICCAI2010 - 13th International Conference, Proceedings",

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Kaynig, V, Fuchs, TJ & Buhmann, JM 2010, Geometrical consistent 3D tracing of neuronal processes in ssTEM data. in Medical Image Computing and Computer-Assisted Intervention, MICCAI2010 - 13th International Conference, Proceedings. PART 2 edn, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), no. PART 2, vol. 6362 LNCS, pp. 209-216, 13th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2010, Beijing, China, 20/09/10. https://doi.org/10.1007/978-3-642-15745-5_26

Geometrical consistent 3D tracing of neuronal processes in ssTEM data. / Kaynig, Verena; Fuchs, Thomas J.; Buhmann, Joachim M.
Medical Image Computing and Computer-Assisted Intervention, MICCAI2010 - 13th International Conference, Proceedings. PART 2. ed. 2010. p. 209-216 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6362 LNCS, No. PART 2).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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AB - In neuroanatomy, automatic geometry extraction of neurons from electron microscopy images is becoming one of the main limiting factors in getting new insights into the functional structure of the brain. We propose a novel framework for tracing neuronal processes over serial sections for 3d reconstructions. The automatic processing pipeline combines the probabilistic output of a random forest classifier with geometrical consistency constraints which take the geometry of whole sections into account. Our experiments demonstrate significant improvement over grouping by Euclidean distance, reducing the split and merge error per object by a factor of two.

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Kaynig V, Fuchs TJ, Buhmann JM. Geometrical consistent 3D tracing of neuronal processes in ssTEM data. In Medical Image Computing and Computer-Assisted Intervention, MICCAI2010 - 13th International Conference, Proceedings. PART 2 ed. 2010. p. 209-216. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); PART 2). doi: 10.1007/978-3-642-15745-5_26

Geometrical consistent 3D tracing of neuronal processes in ssTEM data

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