Molecular and spatial analysis of ganglion cells on retinal flatmounts identifies perivascular neurons resilient to glaucoma

Summary: Processed datasets from applying MERFISH spatial transcriptomics to wholemount retina. Raw imaging data will be hosted at a separate link. Uploaded Data: Anndata objects 1.merged_control.h5adRRaw concatenated cell by gene matrices across many retinae 2. merged_control_cluster_final_mapped.h5adFinal preprocessed cell by gene matrix. 3. RGC_control_mapped.h5adRGC only preprocessed matrix (a subset of the dataset above) 4. Melanopsin_runs.h5ad Processed RGC matrix of MERFISH runs with Melanopsin antibody staining (Cellbound3 column in adata.obs) Additional supplementary data 5. column_info.txtDescription of metadata in columns of .h5ad files. The most important columns are: 'final_x', 'final_y' (spatial coordinates of cells), 'run' (Retina ID), 'region' (Tissue section ID), 'class' (Cell class), 'final_assignment': (Cell type assignment). 6. Spline_coordinates.jsonSplines for the outline of each retina used in certain figures (e.g. Figure S6) 7. Exclusion_areas.zipFor Figure S7 (mosaic analysis). Contains json files, one for each ROI, containing polygons for ROI bounds as well as outlining major holes. 8. Column_mapping.csv and distances.csv Used for all SOHU and control perivascular statistics (Figure 5,6,S6)摘要： 本数据集为将多重误差稳健荧光原位杂交（MERFISH）空间转录组学技术应用于全视网膜铺片后的处理后数据。原始成像数据将通过单独链接发布。 上传数据： Anndata 数据对象 1. merged_control.h5ad：跨多个视网膜拼接的细胞-基因原始整合矩阵 2. merged_control_cluster_final_mapped.h5ad：最终预处理完成的细胞-基因矩阵 3. RGC_control_mapped.h5ad：仅包含视网膜神经节细胞（Retinal Ganglion Cell, RGC）的预处理矩阵（为上述数据集的子集） 4. Melanopsin_runs.h5ad：带有视黑质抗体染色的MERFISH实验视网膜神经节细胞处理后矩阵（adata.obs中的Cellbound3列为相关标记列） 附加补充数据 5. column_info.txt：.h5ad文件各列的元数据说明文档。核心列包括：'final_x'、'final_y'（细胞空间坐标）、'run'（视网膜ID）、'region'（组织切片ID）、'class'（细胞类别）、'final_assignment'（细胞类型注释结果）。 6. Spline_coordinates.json：用于部分图示（如图S6）中各视网膜轮廓的样条曲线坐标数据 7. Exclusion_areas.zip：用于图S7（镶嵌分析）的压缩包，内含多个JSON文件，每个文件对应一个感兴趣区域（Region of Interest, ROI），包含该ROI的边界及主要孔洞轮廓的多边形数据 8. Column_mapping.csv 与 distances.csv：用于所有SOHU及对照组血管周统计分析（对应图5、6、S6）