1. An end-to-end workflow for nondestructive 3D pathology
- Author
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Bishop, Kevin W., Erion Barner, Lindsey A., Han, Qinghua, Baraznenok, Elena, Lan, Lydia, Poudel, Chetan, Gao, Gan, Serafin, Robert B., Chow, Sarah S. L., Glaser, Adam K., Janowczyk, Andrew, Brenes, David, Huang, Hongyi, Miyasato, Dominie, True, Lawrence D., Kang, Soyoung, Vaughan, Joshua C., and Liu, Jonathan T. C.
- Abstract
Recent advances in 3D pathology offer the ability to image orders of magnitude more tissue than conventional pathology methods while also providing a volumetric context that is not achievable with 2D tissue sections, and all without requiring destructive tissue sectioning. Generating high-quality 3D pathology datasets on a consistent basis, however, is not trivial and requires careful attention to a series of details during tissue preparation, imaging and initial data processing, as well as iterative optimization of the entire process. Here, we provide an end-to-end procedure 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. Although 3D pathology is compatible with diverse staining protocols and computationally generated color palettes for visual analysis, this protocol focuses on the use of a fluorescent analog of hematoxylin and eosin, which remains the most common stain used for gold-standard pathological reports. We present our guidelines for a broad range of end users (e.g., biologists, clinical researchers and engineers) in a simple format. The end-to-end workflow requires 3–6 d to complete, bearing in mind that data analysis may take longer.
- Published
- 2024
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