Standardization of size, shape and internal structure of spinal cord images: comparison of three transformation methods.

Functional fluorescence imaging has been widely applied to analyze spatio-temporal patterns of cellular dynamics in the brain and spinal cord. However, it is difficult to integrate spatial information obtained from imaging data in specific regions of interest across multiple samples, due to large va...

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Autores principales:	Yasuhisa Fujiki, Shigefumi Yokota, Yasumasa Okada, Yoshitaka Oku, Yoshiyasu Tamura, Makio Ishiguro, Fumikazu Miwakeichi
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/1a6dff5b58294af3a25a4e7320a3a3d4
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id	oai:doaj.org-article:1a6dff5b58294af3a25a4e7320a3a3d4
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spelling	oai:doaj.org-article:1a6dff5b58294af3a25a4e7320a3a3d42021-11-18T08:48:24ZStandardization of size, shape and internal structure of spinal cord images: comparison of three transformation methods.1932-620310.1371/journal.pone.0076415https://doaj.org/article/1a6dff5b58294af3a25a4e7320a3a3d42013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24223702/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Functional fluorescence imaging has been widely applied to analyze spatio-temporal patterns of cellular dynamics in the brain and spinal cord. However, it is difficult to integrate spatial information obtained from imaging data in specific regions of interest across multiple samples, due to large variability in the size, shape and internal structure of samples. To solve this problem, we attempted to standardize transversely sectioned spinal cord images focusing on the laminar structure in the gray matter. We employed three standardization methods, the affine transformation (AT), the angle-dependent transformation (ADT) and the combination of these two methods (AT+ADT). The ADT is a novel non-linear transformation method developed in this study to adjust an individual image onto the template image in the polar coordinate system. We next compared the accuracy of these three standardization methods. We evaluated two indices, i.e., the spatial distribution of pixels that are not categorized to any layer and the error ratio by the leave-one-out cross validation method. In this study, we used neuron-specific marker (NeuN)-stained histological images of transversely sectioned cervical spinal cord slices (21 images obtained from 4 rats) to create the standard atlas and also to serve for benchmark tests. We found that the AT+ADT outperformed other two methods, though the accuracy of each method varied depending on the layer. This novel image standardization technique would be applicable to optical recording such as voltage-sensitive dye imaging, and will enable statistical evaluations of neural activation across multiple samples.Yasuhisa FujikiShigefumi YokotaYasumasa OkadaYoshitaka OkuYoshiyasu TamuraMakio IshiguroFumikazu MiwakeichiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 11, p e76415 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yasuhisa Fujiki Shigefumi Yokota Yasumasa Okada Yoshitaka Oku Yoshiyasu Tamura Makio Ishiguro Fumikazu Miwakeichi Standardization of size, shape and internal structure of spinal cord images: comparison of three transformation methods.
description	Functional fluorescence imaging has been widely applied to analyze spatio-temporal patterns of cellular dynamics in the brain and spinal cord. However, it is difficult to integrate spatial information obtained from imaging data in specific regions of interest across multiple samples, due to large variability in the size, shape and internal structure of samples. To solve this problem, we attempted to standardize transversely sectioned spinal cord images focusing on the laminar structure in the gray matter. We employed three standardization methods, the affine transformation (AT), the angle-dependent transformation (ADT) and the combination of these two methods (AT+ADT). The ADT is a novel non-linear transformation method developed in this study to adjust an individual image onto the template image in the polar coordinate system. We next compared the accuracy of these three standardization methods. We evaluated two indices, i.e., the spatial distribution of pixels that are not categorized to any layer and the error ratio by the leave-one-out cross validation method. In this study, we used neuron-specific marker (NeuN)-stained histological images of transversely sectioned cervical spinal cord slices (21 images obtained from 4 rats) to create the standard atlas and also to serve for benchmark tests. We found that the AT+ADT outperformed other two methods, though the accuracy of each method varied depending on the layer. This novel image standardization technique would be applicable to optical recording such as voltage-sensitive dye imaging, and will enable statistical evaluations of neural activation across multiple samples.
format	article
author	Yasuhisa Fujiki Shigefumi Yokota Yasumasa Okada Yoshitaka Oku Yoshiyasu Tamura Makio Ishiguro Fumikazu Miwakeichi
author_facet	Yasuhisa Fujiki Shigefumi Yokota Yasumasa Okada Yoshitaka Oku Yoshiyasu Tamura Makio Ishiguro Fumikazu Miwakeichi
author_sort	Yasuhisa Fujiki
title	Standardization of size, shape and internal structure of spinal cord images: comparison of three transformation methods.
title_short	Standardization of size, shape and internal structure of spinal cord images: comparison of three transformation methods.
title_full	Standardization of size, shape and internal structure of spinal cord images: comparison of three transformation methods.
title_fullStr	Standardization of size, shape and internal structure of spinal cord images: comparison of three transformation methods.
title_full_unstemmed	Standardization of size, shape and internal structure of spinal cord images: comparison of three transformation methods.
title_sort	standardization of size, shape and internal structure of spinal cord images: comparison of three transformation methods.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/1a6dff5b58294af3a25a4e7320a3a3d4
work_keys_str_mv	AT yasuhisafujiki standardizationofsizeshapeandinternalstructureofspinalcordimagescomparisonofthreetransformationmethods AT shigefumiyokota standardizationofsizeshapeandinternalstructureofspinalcordimagescomparisonofthreetransformationmethods AT yasumasaokada standardizationofsizeshapeandinternalstructureofspinalcordimagescomparisonofthreetransformationmethods AT yoshitakaoku standardizationofsizeshapeandinternalstructureofspinalcordimagescomparisonofthreetransformationmethods AT yoshiyasutamura standardizationofsizeshapeandinternalstructureofspinalcordimagescomparisonofthreetransformationmethods AT makioishiguro standardizationofsizeshapeandinternalstructureofspinalcordimagescomparisonofthreetransformationmethods AT fumikazumiwakeichi standardizationofsizeshapeandinternalstructureofspinalcordimagescomparisonofthreetransformationmethods
_version_	1718421248203030528

Standardization of size, shape and internal structure of spinal cord images: comparison of three transformation methods.

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