Dataset Information

Multiplex, quantitative cellular analysis in large tissue volumes with clearing-enhanced 3D microscopy (C_e3D).

ABSTRACT: Organ homeostasis, cellular differentiation, signal relay, and in situ function all depend on the spatial organization of cells in complex tissues. For this reason, comprehensive, high-resolution mapping of cell positioning, phenotypic identity, and functional state in the context of macroscale tissue structure is critical to a deeper understanding of diverse biological processes. Here we report an easy to use method, clearing-enhanced 3D (C_e3D), which generates excellent tissue transparency for most organs, preserves cellular morphology and protein fluorescence, and is robustly compatible with antibody-based immunolabeling. This enhanced signal quality and capacity for extensive probe multiplexing permits quantitative analysis of distinct, highly intermixed cell populations in intact C_e3D-treated tissues via 3D histo-cytometry. We use this technology to demonstrate large-volume, high-resolution microscopy of diverse cell types in lymphoid and nonlymphoid organs, as well as to perform quantitative analysis of the composition and tissue distribution of multiple cell populations in lymphoid tissues. Combined with histo-cytometry, C_e3D provides a comprehensive strategy for volumetric quantitative imaging and analysis that bridges the gap between conventional section imaging and disassociation-based techniques.

SUBMITTER: Li W

PROVIDER: S-EPMC5584454 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

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Publications

Multiplex, quantitative cellular analysis in large tissue volumes with clearing-enhanced 3D microscopy (C<sub>e</sub>3D).

Li Weizhe W Germain Ronald N RN Gerner Michael Y MY

Proceedings of the National Academy of Sciences of the United States of America 20170814 35

Organ homeostasis, cellular differentiation, signal relay, and in situ function all depend on the spatial organization of cells in complex tissues. For this reason, comprehensive, high-resolution mapping of cell positioning, phenotypic identity, and functional state in the context of macroscale tissue structure is critical to a deeper understanding of diverse biological processes. Here we report an easy to use method, clearing-enhanced 3D (C<sub>e</sub>3D), which generates excellent tissue trans ...[more]

PMID: 28808033

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Project description:BackgroundPrevious quantitative synthetic MRI of the brain has been solely performed in 2D.PurposeTo evaluate the feasibility of the recently developed sequence 3D-QALAS for brain cortical thickness and volumetric analysis.Study typeReproducibility/repeatability study.SubjectsTwenty-one healthy volunteers (35.6 ± 13.8 years).Field strength/sequence3D T1 -weighted fast spoiled gradient recalled echo (FSPGR) sequence was performed once, and 3D-QALAS sequence was performed twice with a 3T scanner.AssessmentFreeSurfer and FIRST were used to measure cortical thickness and volume of subcortical structures, respectively. Agreement with FSPGR and scan-rescan repeatability were evaluated for 3D-QALAS.Statistical testsPercent relative difference and intraclass correlation coefficient (ICC) were used to assess reproducibility and scan-rescan repeatability of the 3D-QALAS sequence-derived measurements.ResultsPercent relative difference compared with FSPGR in cortical thickness of the whole cortex was 3.1%, and 89% of the regional areas showed less than 10% relative difference in cortical thickness. The mean ICC across all regions was 0.65, and 74% of the structures showed substantial to almost perfect agreement. For volumes of subcortical structures, the median percent relative differences were lower than 10% across all subcortical structures, except for the accumbens area, and all structures showed ICCs of substantial to almost perfect agreement. For the scan-rescan test, percent relative difference in cortical thickness of the whole cortex was 2.3%, and 97% of the regional areas showed less than 10% relative difference in cortical thickness. The mean ICC across all regions was 0.73, and 80% showed substantial to almost perfect agreement. For volumes of subcortical structures, relative differences were less than 10% across all subcortical structures except for the accumbens area, and all structures showed ICCs of substantial to almost perfect agreement.Data conclusion3D-QALAS could be reliably used for measuring cortical thickness and subcortical volumes in most brain regions.Level of evidence3 Technical Efficacy: Stage 1 J. Magn. Reson. Imaging 2019;50:1834-1842.

Dataset Information

Multiplex, quantitative cellular analysis in large tissue volumes with clearing-enhanced 3D microscopy (C_e3D).

Publications

Multiplex, quantitative cellular analysis in large tissue volumes with clearing-enhanced 3D microscopy (C<sub>e</sub>3D).

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Dataset Information

Multiplex, quantitative cellular analysis in large tissue volumes with clearing-enhanced 3D microscopy (Ce3D).

Publications

Multiplex, quantitative cellular analysis in large tissue volumes with clearing-enhanced 3D microscopy (C<sub>e</sub>3D).

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Multiplex, quantitative cellular analysis in large tissue volumes with clearing-enhanced 3D microscopy (C_e3D).