Model-based Vasculature Extraction from Optical Fluorescence Cryomicrotome Images

Ayush Goyal; Jack Lee; Pablo Lamata de la Orden; J. van den Wijngaard; P. van Horssen; J. Spaan; M. Siebes; V. Grau; Nicolas Smith

doi:10.1109/TMI.2012.2227275

Model-based Vasculature Extraction from Optical Fluorescence Cryomicrotome Images

Ayush Goyal, Jack Lee, Pablo Lamata de la Orden, J. van den Wijngaard, P. van Horssen, J. Spaan, M. Siebes, V. Grau, Nicolas Smith

Research output: Contribution to journal › Article › peer-review

31 Citations (Scopus)

Abstract

The aim of this study was to develop a novel method to reconstruct three-dimensional coronary vasculature from cryomicrotome images, comprised of two distinct sets of data fluorescent microsphere beads and coronary vasculature. Fluorescent beads and cast injected into the vasculature were separately imaged with different filter settings to obtain the microsphere and vascular data, respectively. To extract the vascular anatomy, light scattering in the tissue was modelled using a point spread function (PSF). The PSF was parametrized by optical tissue excitation and emission attenuation coefficients, which were estimated by fitting simulated images of microspheres convolved with the PSF model to the experimental microsphere images. These parameters were then applied within a new model-based method for vessel radius estimation. Current state-of-the-art radii estimation methods and the proposed model-based method were applied on vessel phantoms. In this validation study, the Full-Width Half Maximum method of radii estimation, when performed on the raw data without correcting for the optical blurring, resulted in 42.9% error on average for the 170ìm vessel. In comparison, the model-based method resulted in 0.6% error on average for the same phantom. Whole-organ porcine coronary vasculature was automatically reconstructed with the new model-based vascular extraction method.

Original language	English
Number of pages	1
Journal	Ieee Transactions on Medical Imaging
Issue number	99
DOIs	https://doi.org/10.1109/TMI.2012.2227275
Publication status	Accepted/In press - 15 Nov 2012

Keywords

cryomicrotome imaging
three-dimensional automatic reconstruction
whole-organ coronary vasculature
vascular extraction

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@article{48a0ca37bf214be5bfb875875048e7aa,

title = "Model-based Vasculature Extraction from Optical Fluorescence Cryomicrotome Images",

abstract = "The aim of this study was to develop a novel method to reconstruct three-dimensional coronary vasculature from cryomicrotome images, comprised of two distinct sets of data fluorescent microsphere beads and coronary vasculature. Fluorescent beads and cast injected into the vasculature were separately imaged with different filter settings to obtain the microsphere and vascular data, respectively. To extract the vascular anatomy, light scattering in the tissue was modelled using a point spread function (PSF). The PSF was parametrized by optical tissue excitation and emission attenuation coefficients, which were estimated by fitting simulated images of microspheres convolved with the PSF model to the experimental microsphere images. These parameters were then applied within a new model-based method for vessel radius estimation. Current state-of-the-art radii estimation methods and the proposed model-based method were applied on vessel phantoms. In this validation study, the Full-Width Half Maximum method of radii estimation, when performed on the raw data without correcting for the optical blurring, resulted in 42.9% error on average for the 170{\`i}m vessel. In comparison, the model-based method resulted in 0.6% error on average for the same phantom. Whole-organ porcine coronary vasculature was automatically reconstructed with the new model-based vascular extraction method.",

keywords = "cryomicrotome imaging, three-dimensional automatic reconstruction , whole-organ coronary vasculature, vascular extraction ",

author = "Ayush Goyal and Jack Lee and {Lamata de la Orden}, Pablo and {van den Wijngaard}, J. and {van Horssen}, P. and J. Spaan and M. Siebes and V. Grau and Nicolas Smith",

year = "2012",

month = nov,

day = "15",

doi = "10.1109/TMI.2012.2227275",

language = "English",

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AU - Goyal, Ayush

AU - Lee, Jack

AU - Lamata de la Orden, Pablo

AU - van den Wijngaard, J.

AU - van Horssen, P.

AU - Spaan, J.

AU - Siebes, M.

AU - Grau, V.

AU - Smith, Nicolas

PY - 2012/11/15

Y1 - 2012/11/15

N2 - The aim of this study was to develop a novel method to reconstruct three-dimensional coronary vasculature from cryomicrotome images, comprised of two distinct sets of data fluorescent microsphere beads and coronary vasculature. Fluorescent beads and cast injected into the vasculature were separately imaged with different filter settings to obtain the microsphere and vascular data, respectively. To extract the vascular anatomy, light scattering in the tissue was modelled using a point spread function (PSF). The PSF was parametrized by optical tissue excitation and emission attenuation coefficients, which were estimated by fitting simulated images of microspheres convolved with the PSF model to the experimental microsphere images. These parameters were then applied within a new model-based method for vessel radius estimation. Current state-of-the-art radii estimation methods and the proposed model-based method were applied on vessel phantoms. In this validation study, the Full-Width Half Maximum method of radii estimation, when performed on the raw data without correcting for the optical blurring, resulted in 42.9% error on average for the 170ìm vessel. In comparison, the model-based method resulted in 0.6% error on average for the same phantom. Whole-organ porcine coronary vasculature was automatically reconstructed with the new model-based vascular extraction method.

AB - The aim of this study was to develop a novel method to reconstruct three-dimensional coronary vasculature from cryomicrotome images, comprised of two distinct sets of data fluorescent microsphere beads and coronary vasculature. Fluorescent beads and cast injected into the vasculature were separately imaged with different filter settings to obtain the microsphere and vascular data, respectively. To extract the vascular anatomy, light scattering in the tissue was modelled using a point spread function (PSF). The PSF was parametrized by optical tissue excitation and emission attenuation coefficients, which were estimated by fitting simulated images of microspheres convolved with the PSF model to the experimental microsphere images. These parameters were then applied within a new model-based method for vessel radius estimation. Current state-of-the-art radii estimation methods and the proposed model-based method were applied on vessel phantoms. In this validation study, the Full-Width Half Maximum method of radii estimation, when performed on the raw data without correcting for the optical blurring, resulted in 42.9% error on average for the 170ìm vessel. In comparison, the model-based method resulted in 0.6% error on average for the same phantom. Whole-organ porcine coronary vasculature was automatically reconstructed with the new model-based vascular extraction method.

KW - cryomicrotome imaging

KW - three-dimensional automatic reconstruction

KW - whole-organ coronary vasculature

KW - vascular extraction

U2 - 10.1109/TMI.2012.2227275

DO - 10.1109/TMI.2012.2227275

M3 - Article

SN - 0278-0062

JO - Ieee Transactions on Medical Imaging

JF - Ieee Transactions on Medical Imaging

IS - 99

ER -

Model-based Vasculature Extraction from Optical Fluorescence Cryomicrotome Images

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Keywords

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