Posture matching and elastic registration of a mouse atlas to surface topography range data

A. Joshi, Abhijit Chaudhari, Changqing Li, D. W. Shattuck, J. Dutta, R. M. Leahy, A. W. Toga

Research output: Chapter in Book/Report/Conference proceedingConference contribution

12 Citations (Scopus)

Abstract

Estimation of internal mouse anatomy is required for quantitative bioluminescence or fluorescence tomography. However, only surface range data can be recovered from all-optical systems. These data are at times sparse or incomplete. We present a method for fitting an elastically deformable mouse atlas to surface topographic range data acquired by an optical system. In this method, we first match the postures of a deformable atlas and the range data of the mouse being imaged. This is achieved by aligning manually identified landmarks. We then minimize the asymmetric L2 pseudo-distance between the surface of the deformable atlas and the surface topography range data. Once this registration is accomplished, the internal anatomy of the atlas is transformed to the coordinate system of the range data using elastic energy minimization. We evaluated our method by using it to register a digital mouse atlas to a surface model produced from a manually labeled CT mouse data set. Dice coefficents indicated excellent agreement in the brain and heart, with fair agreement in the kidneys and bladder. We also present example results produced using our method to align the digital mouse atlas to surface range data.

Original languageEnglish (US)
Title of host publicationProceedings - 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009
Pages366-369
Number of pages4
DOIs
StatePublished - 2009
Event2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009 - Boston, MA, United States
Duration: Jun 28 2009Jul 1 2009

Other

Other2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009
CountryUnited States
CityBoston, MA
Period6/28/097/1/09

Fingerprint

Atlases
Surface topography
Posture
Optical Devices
Optical systems
Anatomy
Bioluminescence
Tomography
Brain
Information Systems
Fluorescence
Urinary Bladder
Kidney

Keywords

  • Deformable atlas
  • Mouse registration
  • Optical tomography

ASJC Scopus subject areas

  • Biomedical Engineering
  • Radiology Nuclear Medicine and imaging

Cite this

Joshi, A., Chaudhari, A., Li, C., Shattuck, D. W., Dutta, J., Leahy, R. M., & Toga, A. W. (2009). Posture matching and elastic registration of a mouse atlas to surface topography range data. In Proceedings - 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009 (pp. 366-369). [5193060] https://doi.org/10.1109/ISBI.2009.5193060

Posture matching and elastic registration of a mouse atlas to surface topography range data. / Joshi, A.; Chaudhari, Abhijit; Li, Changqing; Shattuck, D. W.; Dutta, J.; Leahy, R. M.; Toga, A. W.

Proceedings - 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009. 2009. p. 366-369 5193060.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Joshi, A, Chaudhari, A, Li, C, Shattuck, DW, Dutta, J, Leahy, RM & Toga, AW 2009, Posture matching and elastic registration of a mouse atlas to surface topography range data. in Proceedings - 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009., 5193060, pp. 366-369, 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009, Boston, MA, United States, 6/28/09. https://doi.org/10.1109/ISBI.2009.5193060
Joshi A, Chaudhari A, Li C, Shattuck DW, Dutta J, Leahy RM et al. Posture matching and elastic registration of a mouse atlas to surface topography range data. In Proceedings - 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009. 2009. p. 366-369. 5193060 https://doi.org/10.1109/ISBI.2009.5193060
Joshi, A. ; Chaudhari, Abhijit ; Li, Changqing ; Shattuck, D. W. ; Dutta, J. ; Leahy, R. M. ; Toga, A. W. / Posture matching and elastic registration of a mouse atlas to surface topography range data. Proceedings - 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009. 2009. pp. 366-369
@inproceedings{345183d4fd2a491baf9af47cfcdaff76,
title = "Posture matching and elastic registration of a mouse atlas to surface topography range data",
abstract = "Estimation of internal mouse anatomy is required for quantitative bioluminescence or fluorescence tomography. However, only surface range data can be recovered from all-optical systems. These data are at times sparse or incomplete. We present a method for fitting an elastically deformable mouse atlas to surface topographic range data acquired by an optical system. In this method, we first match the postures of a deformable atlas and the range data of the mouse being imaged. This is achieved by aligning manually identified landmarks. We then minimize the asymmetric L2 pseudo-distance between the surface of the deformable atlas and the surface topography range data. Once this registration is accomplished, the internal anatomy of the atlas is transformed to the coordinate system of the range data using elastic energy minimization. We evaluated our method by using it to register a digital mouse atlas to a surface model produced from a manually labeled CT mouse data set. Dice coefficents indicated excellent agreement in the brain and heart, with fair agreement in the kidneys and bladder. We also present example results produced using our method to align the digital mouse atlas to surface range data.",
keywords = "Deformable atlas, Mouse registration, Optical tomography",
author = "A. Joshi and Abhijit Chaudhari and Changqing Li and Shattuck, {D. W.} and J. Dutta and Leahy, {R. M.} and Toga, {A. W.}",
year = "2009",
doi = "10.1109/ISBI.2009.5193060",
language = "English (US)",
isbn = "9781424439324",
pages = "366--369",
booktitle = "Proceedings - 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009",

}

TY - GEN

T1 - Posture matching and elastic registration of a mouse atlas to surface topography range data

AU - Joshi, A.

AU - Chaudhari, Abhijit

AU - Li, Changqing

AU - Shattuck, D. W.

AU - Dutta, J.

AU - Leahy, R. M.

AU - Toga, A. W.

PY - 2009

Y1 - 2009

N2 - Estimation of internal mouse anatomy is required for quantitative bioluminescence or fluorescence tomography. However, only surface range data can be recovered from all-optical systems. These data are at times sparse or incomplete. We present a method for fitting an elastically deformable mouse atlas to surface topographic range data acquired by an optical system. In this method, we first match the postures of a deformable atlas and the range data of the mouse being imaged. This is achieved by aligning manually identified landmarks. We then minimize the asymmetric L2 pseudo-distance between the surface of the deformable atlas and the surface topography range data. Once this registration is accomplished, the internal anatomy of the atlas is transformed to the coordinate system of the range data using elastic energy minimization. We evaluated our method by using it to register a digital mouse atlas to a surface model produced from a manually labeled CT mouse data set. Dice coefficents indicated excellent agreement in the brain and heart, with fair agreement in the kidneys and bladder. We also present example results produced using our method to align the digital mouse atlas to surface range data.

AB - Estimation of internal mouse anatomy is required for quantitative bioluminescence or fluorescence tomography. However, only surface range data can be recovered from all-optical systems. These data are at times sparse or incomplete. We present a method for fitting an elastically deformable mouse atlas to surface topographic range data acquired by an optical system. In this method, we first match the postures of a deformable atlas and the range data of the mouse being imaged. This is achieved by aligning manually identified landmarks. We then minimize the asymmetric L2 pseudo-distance between the surface of the deformable atlas and the surface topography range data. Once this registration is accomplished, the internal anatomy of the atlas is transformed to the coordinate system of the range data using elastic energy minimization. We evaluated our method by using it to register a digital mouse atlas to a surface model produced from a manually labeled CT mouse data set. Dice coefficents indicated excellent agreement in the brain and heart, with fair agreement in the kidneys and bladder. We also present example results produced using our method to align the digital mouse atlas to surface range data.

KW - Deformable atlas

KW - Mouse registration

KW - Optical tomography

UR - http://www.scopus.com/inward/record.url?scp=70449362062&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=70449362062&partnerID=8YFLogxK

U2 - 10.1109/ISBI.2009.5193060

DO - 10.1109/ISBI.2009.5193060

M3 - Conference contribution

SN - 9781424439324

SP - 366

EP - 369

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

ER -