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。借助荧光非线性显微镜（fluorescence nonlinear microscopy, NLM）与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结构的三维（3D）可视化。本研究对12名患者的存档肾脏石蜡包埋块进行脱蜡处理，使用Hoechst与伊红（Eosin）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）完成光学透明化。完整活检组织块（厚度范围88~660微米）的非线性显微镜成像采用NLM完成，将荧光信号映射至苏木精-伊红（H&E）配色标尺。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）进行三维分割，并可获取其体积、直径及构成百分比。三维NLM成像中的肾小球计数较高，这表明存档石蜡包埋块可作为大规模回顾性研究的丰富组织资源。快速光学透明化与NLM成像技术……已收集存档肾脏活检石蜡包埋块。对样本进行脱蜡、光学透明化处理，并使用Hoechst 33342与伊红Y（eosin Y）进行染色。采用双通道双光子激发荧光显微镜结合XYZ方向的连续拼接扫描，完成染色样本的三维数字化成像。详细实验方案请参见材料与方法部分。

# 配套于《利用非线性显微镜技术从存档肾脏活检样本中获取数据》一文的图像数据集

本提交数据包包含了题为《利用非线性显微镜技术从存档肾脏活检样本中获取数据》（发表于PLOS ONE，Cahill等人，2024年）的论文中所有用于生成图表的荧光显微镜原始数据集。原始文件为二维图像瓦片（2D tiles）数据流，将这些拼接块整合后，可形成存档肾脏活检样本的三维显微可视化模型。为方便使用，我们还提供了预拼接完成的全分辨率、全位深双通道图像栈。

**数据集编号：论文图表编号：数据集描述**
LC-6-2：图1：晚期糖尿病肾病患者活检样本图像
LC-7-2-rdo2：图3与图4：显示局灶节段性肾小球硬化伴塌陷性肾小球病特征的活检样本图像
LC-9-1-rdo：图5：显示新月体性IgA肾病的活检样本图像
LC-10-1：图2：确诊为……患者的活检样本图像