Dataset Information

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

ABSTRACT: 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 mm³ 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 µm³ 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.

SUBMITTER: Nicolas N

PROVIDER: S-EPMC8620055 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Multi-modal imaging, by light-microscopy (LM) and Magnetic Resonance Imaging (MRI), holds promise for examining the brain across various resolutions and scales. While MRI acquires images in three dimensions, acquisition of intact whole-brain by LM requires a process of tissue clearing that renders the brain transparent. Removal of lipids (delipidation) is a critical step in the tissue clearing process, and was previsouly suggested to be the cause for absence of MRI contrast in cleared brains. Yet, the association between MRI contrast, delipidation and the different clearing techniques is debatable. Here, we provide datasets concerning lipid-content in cleared brain tissues obtained by various approaches. Fixed mouse and rat brains were cleared by CLARITY, Scale, uDISCO and ECi clearing techniques. Lipid-content was assessed at various intermediate steps of the different clearing methods, as well as at the end of the processes. Methods employed included whole brain MRI acquisition, Oil Red O (ORO)- and carbocyanine DiI-staining of cryosections, and DiI-washout assay from brain slices. MRI contrast-to-noise ratio, staining intensities and integrity of tissue were systematically analyzed. We demonstrate that lipid electrophoresis, an essential step of the CLARITY approach, engenders progressive reduction in MRI contrast in non-cleared (PFA-fixed) control brains, as well as strongly reduces contrast from uDISCO and ECi-cleared brains. ORO minimally stained CLARITY-cleared brains, however efficiently labelled uDISCO and ECi-cleared brains. Conversely, and in contrast to ORO-staining, DiI equally stained control, CLARITY, ECi and uDISCO-cleared brains. Both ORO- and DiI-staining demonstrated impairment in brain tissue integrity following CLARITY, but less so in uDISCO and ECi brains. DiI-washout assay demonstrated that each of the solvents employed along the process of uDISCO and ECi are highly delipidating, as well as the SDS-electrophoresis employed during CLARITY clearing. However, Scale treatment preserved most of the DiI dye. These data emphasize the variability in lipid assessment of cleared tissues by common techniques, and may help to resolve the contribution of lipids in brain MRI contrast.

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Dataset Information

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

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