An end-to-end workflow for non-destructive 3D pathology
Bishop, K. W.; Barner, L. A. E.; Han, Q.; Baraznenok, E.; Lan, L.; Poudel, C.; Gao, G.; Serafin, R. B.; Chow, S. S. L.; Glaser, A. K.; Janowczyk, A.; Brenes, D.; Huang, H.; Miyasato, D.; True, L. D.; Kang, S.; Vaughan, J. C.; Liu, J. T. C.
Show 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.
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