Rakaia: interactive discovery of spatial biology at scale

This repository contains the raw data for the paper Rakaia: interactive discovery of spatial biology at scale- zip bundle raw_xenium_fig_1.zip contains the raw Xenium outputs for Extended Data Fig 1: https://github.com/camlab-bioml/2025-rakaia-paper-analysis/tree/main/extended_data_fig_1 - zip bundle multimodal_integration_fig_1.zip contains both the Xenium morphology focus images and matched IMC ROI to the raw Xenium outputs for the integrated field of view (FOV) in Extended Data Fig 1: https://github.com/camlab-bioml/2025-rakaia-paper-analysis/tree/main/extended_data_fig_1- zip bundle dm_immune_fig_2.zip contains the steinbock IMC pipeline output directory with the raw MCD images and single cell quantification for Main Fig. 2: https://github.com/camlab-bioml/2025-rakaia-paper-analysis/tree/main/fig_2. The predictions for each IMC ROI for hyperplasia are found in the phenotypeSearch column in both dm_immune.h5ad and measurements.csv- zip bundle dm_immune_tiff_fig_2. zip contains the TIFF format of the IMC images in dm_immune_fig_2.zip that appear in Main Fig. 2- More information about the format of the IMC pipeline output can be found here: https://github.com/camlab-bioml/steinbock_snakemake本仓库收录论文《Rakaia：大规模空间生物学交互式发现》的原始数据集。 1. zip压缩包raw_xenium_fig_1.zip 包含补充数据图1的原始Xenium输出结果，相关资源路径为：https://github.com/camlab-bioml/2025-rakaia-paper-analysis/tree/main/extended_data_fig_1。 2. zip压缩包multimodal_integration_fig_1.zip 包含补充数据图1中整合视野（Field of View, FOV）的Xenium形态学聚焦图像，以及与原始Xenium输出匹配的成像质谱流式（Imaging Mass Cytometry, IMC）感兴趣区域（Region of Interest, ROI），相关资源路径同上。 3. zip压缩包dm_immune_fig_2.zip 包含主图2的steinbock IMC分析流程输出目录，内含原始MCD图像与单细胞定量结果，相关资源路径为：https://github.com/camlab-bioml/2025-rakaia-paper-analysis/tree/main/fig_2。各IMC ROI的增生预测结果存储于dm_immune.h5ad与measurements.csv文件的phenotypeSearch列中。 4. zip压缩包dm_immune_tiff_fig_2.zip 包含主图2所用的、源自dm_immune_fig_2.zip的IMC图像的TIFF格式版本。 有关IMC分析流程输出格式的更多详情，请参阅：https://github.com/camlab-bioml/steinbock_snakemake。