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...对肾脏活检样本进行全面检测，有助于加深对肾脏疾病的认知。使用荧光非线性显微镜（fluorescence nonlinear microscopy, NLM）结合光学透明化技术对肾脏活检样本进行成像，可在无需石蜡切片机切片的情况下实现病理学特征的三维可视化。本研究纳入12例患者的存档肾脏石蜡块，经脱蜡处理后，使用Hoechst与伊红进行染色以实现细胞核与细胞质/基质的荧光对比，随后采用苯甲醇-苯甲酸苄酯（benzyl alcohol benzyl benzoate, BABB）进行光学透明化处理。对厚度范围为88~660 μm的完整活检组织片段进行NLM成像，将荧光信号映射至苏木精-伊红（H&E）配色方案。研究人员对囊肿、肾小球、渗出性病变以及基姆斯特尔-威尔逊结节（Kimmelstiel-Wilson nodules）进行了三维分割，并可获取其体积、直径及构成百分比。三维NLM成像下的肾小球计数较高，这表明存档石蜡块可作为丰富的组织资源，支持大规模回顾性研究的开展。快速光学透明化与NLM成像技术…… 本研究收集了存档肾脏活检石蜡块。样本经脱蜡、光学透明化处理后，使用Hoechst 33342与伊红Y进行染色。随后通过双通道双光子激发荧光显微镜，并沿XYZ轴逐次拼接成像，将染色样本进行三维数字化。详细实验方案请参见材料与方法部分。 # 伴随"Data retrieval from archival renal biopsies using nonlinear microscopy"一文的图像数据集 本数据集包含为发表于《PLOS ONE》的论文《Data retrieval from archival renal biopsies using nonlinear microscopy》（Cahill等人，2024年）制作图表所需的全部原始荧光显微镜数据集。原始文件为二维图像块序列，将这些图像块拼接后，可得到存档肾脏活检样本的三维显微可视化结果。为方便使用，我们同时提供了已完成拼接的全分辨率、全位深双通道图像栈。 **数据集名称：论文图表编号：描述** LC-6-2：图1：晚期糖尿病肾病患者的活检样本图像 LC-7-2-rdo2：图3与图4：表现为局灶节段性肾小球硬化并伴有塌陷性肾小球病特征的活检样本图像 LC-9-1-rdo：图5：新月体性IgA肾病患者的活检样本图像 LC-10-1：图2：确诊为……患者的活检样本图像