Automatic alignment of stacks of filament data

V.J. Dercksen; B. Weber; D. Günther; M. Oberlaender; S. Prohaska; H.-C. Hege

doi:10.1109/ISBI.2009.5193216

Automatic alignment of stacks of filament data

V.J. Dercksen
, B. Weber
, D. Günther
, M. Oberlaender
, S. Prohaska
, H.-C. Hege

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

Abstract

We present a fast and robust method for the alignment of image stacks containing filamentous structures. Such stacks are usually obtained by physical sectioning a specimen, followed by an optical sectioning of each slice. For reconstruction, the filaments have to be traced and the sub-volumes aligned. Our algorithm takes traced filaments as input and matches their endpoints to find the optimal transform. We show that our method is able to quickly and accurately align sub-volumes containing neuronal processes, acquired using brightfield microscopy. Our method also makes it possible to align traced microtubuli, obtained from electron tomography data, which are extremely difficult to align manually. © 2009 IEEE.

Original language	English
Title of host publication	Proceedings - 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009
Pages	971-974
DOIs	https://doi.org/10.1109/ISBI.2009.5193216
Publication status	Published - 2009
Externally published	Yes
Event	2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009 - , United States Duration: 28 Jun 2009 → 1 Jul 2009

Conference

Conference	2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009
Country/Territory	United States
Period	28/06/09 → 1/07/09

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10.1109/ISBI.2009.5193216

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@inproceedings{c23bc5cd6ac34aee9fb9b72348489ef8,

title = "Automatic alignment of stacks of filament data",

abstract = "We present a fast and robust method for the alignment of image stacks containing filamentous structures. Such stacks are usually obtained by physical sectioning a specimen, followed by an optical sectioning of each slice. For reconstruction, the filaments have to be traced and the sub-volumes aligned. Our algorithm takes traced filaments as input and matches their endpoints to find the optimal transform. We show that our method is able to quickly and accurately align sub-volumes containing neuronal processes, acquired using brightfield microscopy. Our method also makes it possible to align traced microtubuli, obtained from electron tomography data, which are extremely difficult to align manually. {\textcopyright} 2009 IEEE.",

author = "V.J. Dercksen and B. Weber and D. G{\"u}nther and M. Oberlaender and S. Prohaska and H.-C. Hege",

year = "2009",

doi = "10.1109/ISBI.2009.5193216",

language = "English",

pages = "971--974",

booktitle = "Proceedings - 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009",

note = "2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009 ; Conference date: 28-06-2009 Through 01-07-2009",

}

Dercksen, VJ, Weber, B, Günther, D, Oberlaender, M, Prohaska, S & Hege, H-C 2009, Automatic alignment of stacks of filament data. in Proceedings - 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009. pp. 971-974, 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009, United States, 28/06/09. https://doi.org/10.1109/ISBI.2009.5193216

TY - GEN

T1 - Automatic alignment of stacks of filament data

AU - Dercksen, V.J.

AU - Weber, B.

AU - Günther, D.

AU - Oberlaender, M.

AU - Prohaska, S.

AU - Hege, H.-C.

PY - 2009

Y1 - 2009

N2 - We present a fast and robust method for the alignment of image stacks containing filamentous structures. Such stacks are usually obtained by physical sectioning a specimen, followed by an optical sectioning of each slice. For reconstruction, the filaments have to be traced and the sub-volumes aligned. Our algorithm takes traced filaments as input and matches their endpoints to find the optimal transform. We show that our method is able to quickly and accurately align sub-volumes containing neuronal processes, acquired using brightfield microscopy. Our method also makes it possible to align traced microtubuli, obtained from electron tomography data, which are extremely difficult to align manually. © 2009 IEEE.

AB - We present a fast and robust method for the alignment of image stacks containing filamentous structures. Such stacks are usually obtained by physical sectioning a specimen, followed by an optical sectioning of each slice. For reconstruction, the filaments have to be traced and the sub-volumes aligned. Our algorithm takes traced filaments as input and matches their endpoints to find the optimal transform. We show that our method is able to quickly and accurately align sub-volumes containing neuronal processes, acquired using brightfield microscopy. Our method also makes it possible to align traced microtubuli, obtained from electron tomography data, which are extremely difficult to align manually. © 2009 IEEE.

UR - https://www.scopus.com/pages/publications/70449371000

U2 - 10.1109/ISBI.2009.5193216

DO - 10.1109/ISBI.2009.5193216

M3 - Conference contribution

SP - 971

EP - 974

BT - Proceedings - 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009

T2 - 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009

Y2 - 28 June 2009 through 1 July 2009

ER -

Automatic alignment of stacks of filament data

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