Dataset Information

An end-to-end workflow for non-destructive 3D pathology.

ABSTRACT: Recent advances in 3D pathology offer the ability to image orders-of-magnitude more tissue than conventional pathology while providing a volumetric context that is lacking with 2D tissue sections, all without requiring destructive tissue sectioning. Generating high-quality 3D pathology datasets on a consistent basis is non-trivial, requiring careful attention to many details regarding tissue preparation, imaging, and data/image processing in an iterative process. Here we provide an end-to-end protocol covering all aspects of a 3D pathology workflow (using light-sheet microscopy as an illustrative imaging platform) with sufficient detail to perform well-controlled preclinical and clinical studies. While 3D pathology is compatible with diverse staining protocols and computationally generated color palettes for visual analysis, this protocol will focus on a fluorescent analog of hematoxylin and eosin (H&E), which remains the most common stain for gold-standard diagnostic determinations. We present our guidelines for a broad range of end-users (e.g., biologists, clinical researchers, and engineers) in a simple tutorial format.

SUBMITTER: Bishop KW

PROVIDER: S-EPMC10418226 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature

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An end-to-end workflow for non-destructive 3D pathology.

Bishop Kevin W KW Barner Lindsey A Erion LAE Han Qinghua Q Baraznenok Elena E Lan Lydia L Poudel Chetan C Gao Gan G Serafin Robert B RB Chow Sarah S L SSL Glaser Adam K AK Janowczyk Andrew A Brenes David D Huang Hongyi H Miyasato Dominie D True Lawrence D LD Kang Soyoung S Vaughan Joshua C JC Liu Jonathan T C JTC

bioRxiv : the preprint server for biology 20230806

Recent advances in 3D pathology offer the ability to image orders-of-magnitude more tissue than conventional pathology while providing a volumetric context that is lacking with 2D tissue sections, all without requiring destructive tissue sectioning. Generating high-quality 3D pathology datasets on a consistent basis is non-trivial, requiring careful attention to many details regarding tissue preparation, imaging, and data/image processing in an iterative process. Here we provide an end-to-end pr ...[more]

PMID: 37577615

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Dataset Information

An end-to-end workflow for non-destructive 3D pathology.

Publications

An end-to-end workflow for non-destructive 3D pathology.

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