Data retrieval from archival renal biopsies using nonlinear microscopy

Thorough examination of renal biopsies may improve understanding of renal disease. Imaging of renal biopsies with fluorescence nonlinear microscopy (NLM) and optical clearing enables three-dimensional (3D) visualization of pathology without microtome sectioning. Archival renal paraffin blocks from 12 patients were deparaffinized and stained with Hoechst and Eosin for fluorescent nuclear and cytoplasmic/stromal contrast, then optically cleared using benzyl alcohol benzyl benzoate (BABB). NLM images of entire biopsy fragments (thickness range 88-660 µm) were acquired using NLM with fluorescent signals mapped to an H&E color scale. Cysts, glomeruli, exudative lesions, and Kimmelstiel-Wilson nodules were segmented in 3D and their volumes, diameters, and percent composition could be obtained. The glomerular count on 3D NLM volumes was high indicating that archival blocks could be a vast tissue resource to enable larger-scale retrospective studies. Rapid optical clearing and NLM imaging e..., Archival renal biopsy paraffin blocks were collected. Specimens were deparaffinized, optically cleared, and stained with Hoechst 33342 and eosin Y. Stained specimens were digitized in 3D with dual-channel two-photon excitation fluorescence microscopy and sequential tiling in XYZ.
See Materials and Methods for more detailed protocol information., , # Image datasets accompanying \"Data retrieval from archival renal biopsies using nonlinear microscopy\"

The submission contains all source fluorescence microscopy datasets used to produce figures for the manuscript entitled, \"Data retrieval from archival renal biopsies using nonlinear microscopy\" PLOS ONE (Cahill et al., 2024). The source files are streams of 2D tiles, which when stitched together, form 3D microscopic representations of archival renal biopsies. For convenience, we have also included pre-stitched, full-resolution & bit depth, 2-channel stacks.

**Dataset name: Manuscript figure number: Description**
LC-6-2: Figure 1: Image of a biopsy from a patient with advanced diabetic nephropathy.
LC-7-2-rdo2: Figures 3 & 4: Image of a biopsy showing focal and segmental glomerulosclerosis with features of collapsing glomerulopathy
LC-9-1-rdo: Figure 5: Image of a biopsy showing crescentic IgA nephropathy.
LC-10-1: Figure 2: Image of a biopsy from a patient diagnosed with di...