Computational Identification and 3D Morphological Characterization of Renal Glomeruli in Optically Cleared Murine Kidneys

The aim of this study was to establish an accessible methodology for the objective identification and 3D morphological characterization of renal glomeruli in mice. 3D imaging of the renal cortex was performed by light sheet microscopy on iDISCO+ optical cleared kidneys of six C57BL/6J mice after lab...

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Autores principales:	Nabil Nicolas, Nour Nicolas, Etienne Roux
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	renal glomeruli optical clearing light sheet microscopy 3D imaging 3D image processing 3D morphological characterization Chemical technology TP1-1185
Acceso en línea:	https://doaj.org/article/30246ecb3d9e436eb0622be25da2707a
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spelling	oai:doaj.org-article:30246ecb3d9e436eb0622be25da2707a2021-11-25T18:56:26ZComputational Identification and 3D Morphological Characterization of Renal Glomeruli in Optically Cleared Murine Kidneys10.3390/s212274401424-8220https://doaj.org/article/30246ecb3d9e436eb0622be25da2707a2021-11-01T00:00:00Zhttps://www.mdpi.com/1424-8220/21/22/7440https://doaj.org/toc/1424-8220The aim of this study was to establish an accessible methodology for the objective identification and 3D morphological characterization of renal glomeruli in mice. 3D imaging of the renal cortex was performed by light sheet microscopy on iDISCO+ optical cleared kidneys of six C57BL/6J mice after labelling of the capillary endothelium by lectin injection. 3D images were processed with the open source software ImageJ, and statistical analysis done with GraphPad Prism. Non-visual delimitation of the external surface of the glomeruli was ensured by greyscale-based thresholding, the value of which was determined from the statistical analysis of the voxel frequency distribution. Exclusion of false-positive identification was done by successive volume- and shape-based segmentation. Renal glomeruli were characterized by their number, surface area, volume, and compactness. Average data were expressed as mean ± SD. The number of glomeruli was equal to 283 ± 35 per mm<sup>3</sup> of renal tissue, representing 1.78 ± 0.49% of the tissue volume. The surface area, volume and compactness were equal to 20,830 ± 6200 µm², 62,280 ± 14,000 µm<sup>3</sup> and 0.068 ± 0.026, respectively. The proposed standardized methodology allows the identification of the renal glomeruli and their 3D morphological characterization, and is easily accessible for biologists.Nabil NicolasNour NicolasEtienne RouxMDPI AGarticlerenal glomerulioptical clearinglight sheet microscopy3D imaging3D image processing3D morphological characterizationChemical technologyTP1-1185ENSensors, Vol 21, Iss 7440, p 7440 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	renal glomeruli optical clearing light sheet microscopy 3D imaging 3D image processing 3D morphological characterization Chemical technology TP1-1185
spellingShingle	renal glomeruli optical clearing light sheet microscopy 3D imaging 3D image processing 3D morphological characterization Chemical technology TP1-1185 Nabil Nicolas Nour Nicolas Etienne Roux Computational Identification and 3D Morphological Characterization of Renal Glomeruli in Optically Cleared Murine Kidneys
description	The aim of this study was to establish an accessible methodology for the objective identification and 3D morphological characterization of renal glomeruli in mice. 3D imaging of the renal cortex was performed by light sheet microscopy on iDISCO+ optical cleared kidneys of six C57BL/6J mice after labelling of the capillary endothelium by lectin injection. 3D images were processed with the open source software ImageJ, and statistical analysis done with GraphPad Prism. Non-visual delimitation of the external surface of the glomeruli was ensured by greyscale-based thresholding, the value of which was determined from the statistical analysis of the voxel frequency distribution. Exclusion of false-positive identification was done by successive volume- and shape-based segmentation. Renal glomeruli were characterized by their number, surface area, volume, and compactness. Average data were expressed as mean ± SD. The number of glomeruli was equal to 283 ± 35 per mm<sup>3</sup> of renal tissue, representing 1.78 ± 0.49% of the tissue volume. The surface area, volume and compactness were equal to 20,830 ± 6200 µm², 62,280 ± 14,000 µm<sup>3</sup> and 0.068 ± 0.026, respectively. The proposed standardized methodology allows the identification of the renal glomeruli and their 3D morphological characterization, and is easily accessible for biologists.
format	article
author	Nabil Nicolas Nour Nicolas Etienne Roux
author_facet	Nabil Nicolas Nour Nicolas Etienne Roux
author_sort	Nabil Nicolas
title	Computational Identification and 3D Morphological Characterization of Renal Glomeruli in Optically Cleared Murine Kidneys
title_short	Computational Identification and 3D Morphological Characterization of Renal Glomeruli in Optically Cleared Murine Kidneys
title_full	Computational Identification and 3D Morphological Characterization of Renal Glomeruli in Optically Cleared Murine Kidneys
title_fullStr	Computational Identification and 3D Morphological Characterization of Renal Glomeruli in Optically Cleared Murine Kidneys
title_full_unstemmed	Computational Identification and 3D Morphological Characterization of Renal Glomeruli in Optically Cleared Murine Kidneys
title_sort	computational identification and 3d morphological characterization of renal glomeruli in optically cleared murine kidneys
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/30246ecb3d9e436eb0622be25da2707a
work_keys_str_mv	AT nabilnicolas computationalidentificationand3dmorphologicalcharacterizationofrenalglomeruliinopticallyclearedmurinekidneys AT nournicolas computationalidentificationand3dmorphologicalcharacterizationofrenalglomeruliinopticallyclearedmurinekidneys AT etienneroux computationalidentificationand3dmorphologicalcharacterizationofrenalglomeruliinopticallyclearedmurinekidneys
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Computational Identification and 3D Morphological Characterization of Renal Glomeruli in Optically Cleared Murine Kidneys

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