Modeling development of tertiary lymphoid structures in pulmonary tuberculosis by 3D profiling and trajectory analysis
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This repository hosts an index of data and instructions to access original data associated with "Modeling development of tertiary lymphoid structures in pulmonary tuberculosis by 3D profiling and trajectory analysis". TABLE OF CONTENTS GENERAL INFORMATION ASSOCIATED PUBLICATION RECOMMENDED CITATION USEFUL LINKS FILE ORGANIZATION REPOSITORY LINKS FILE LIST ADDITIONAL NOTES/COMMENTS GENERAL INFORMATION Modeling development of tertiary lymphoid structures in pulmonary tuberculosis by 3D profiling and trajectory analysis Authors: Emmanuel C. Ogbonna, Soheil R. Talemi, Zoltan Maliga, Ziyuan Zhao, Clarence Yapp, Shishir Pant, Yi Daniel Lu, Jeremy Muhlich, Andréanne Gagné, Amanda J. Martinot, Shannon Coy, Sandro Santagata, Angela Shih, Isaac H. Solomon, Threnesan Naidoo, Bree B. Aldridge, Adrie Steyn, Peter K. Sorger† Please cite this data as the following: Ogbonna and Rastgou Talemi (2026). Modeling development of tertiary lymphoid structures in pulmonary tuberculosis by 3D profiling and trajectory analysis. biorxiv https://doi.org/10.64898/2026.06.03.725201 Relevant links: Publication DOI: Associated GitHub Repository: https://github.com/labsyspharm/TB-3D-TLS-2026/ FILE ORGANIZATION: Each file follows the following naming convention: Each folder corresponds to a patient sample (N). File Type Description Location N.ome.tif Stitched multiplex CyCIF image pyramid in ome.tif format AWS N.ome.tif Hematoxylin and Eosin stained image of adjacent FFPE tissue section AWS N.ome.tif Segmentation mask image AWS N.csv single-cell feature table, including intensity data for all channels AWS N.fastq GeoMx Sequencing data GEO N.ims Stitched and registered 3D multiplexed CyCIF image in .ims format AWS AWS Data Access Full-resolution CyCIF images, single cell segmentation masks, and cell count tables will be available via AWS. You will need the following bucket name: lsp-public-data/ogbonna-2026-tb-tls/ For instructions on how to access data from AWS, visit “Access Laboratory of Systems Pharmacology Datasets on AWS” (https://zenodo.org/records/10223574) If you experience issues accessing the above AWS S3 buckets, email tissue-atlas(at)hms.harvard.edu with the subject line "ogbonna-2026-tb-tls: Data Access". GEO Data Access GeoMx gene expression data is available via the Gene Expression Omnibus (GEO): Accession number: GSE318959 Other Repository Image data generated during this study are available on the Gates TB Data Portal (https://idp.tissue-atlas.org/). For access, email tissue-atlas(at)hms.harvard.edu with the subject line "Gates TB Data Portal: Data Access". FILE LIST CyCIF Image Data Patient ID File Name Location File Size (GB) Antibody Panel Patient1_B4 LSP24522.ome.tif AWS 222.37 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24525.ome.tif AWS 202.51 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24528.ome.tif AWS 202.57 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24531.ome.tif AWS 225.94 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24534.ome.tif AWS 220.79 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24537.ome.tif AWS 204.92 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24540.ome.tif AWS 191.57 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24543.ome.tif AWS 213.09 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24546.ome.tif AWS 205.37 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24549.ome.tif AWS 212.91 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24552.ome.tif AWS 199.53 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24555.ome.tif AWS 212.91 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24558.ome.tif AWS 221.39 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24561.ome.tif AWS 217.61 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24564.ome.tif AWS 214.29 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24567.ome.tif AWS 196.63 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24570.ome.tif AWS 207.13 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24573.ome.tif AWS 226.64 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24576.ome.tif AWS 230.50 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24579.ome.tif AWS 205.65 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24582.ome.tif AWS 226.38 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24585.ome.tif AWS 199.04 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24588.ome.tif AWS 215.38 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24591.ome.tif AWS 200.37 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24594.ome.tif AWS 217.11 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24597.ome.tif AWS 199.92 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24600.ome.tif AWS 202.57 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24603.ome.tif AWS 219.74 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24606.ome.tif AWS 219.70 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24609.ome.tif AWS 226.05 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24612.ome.tif AWS 197.44 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24615.ome.tif AWS 222.30 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24618.ome.tif AWS 197.84 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24621.ome.tif AWS 198.85 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24624.ome.tif AWS 198.49 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24627.ome.tif AWS 216.52 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24630.ome.tif AWS 210.79 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24633.ome.tif AWS 193.94 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24636.ome.tif AWS 203.49 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24639.ome.tif AWS 185.99 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B5 LSP16101.ome.tif AWS 214.00 ORION imaging panel Patient1_B5 LSP16102_B5_Scan1.ome.tiff AWS 15.30 p17_e6_TB_Granulomas_GeoMx IF Patient1_B5 LSP16102.ome.tif AWS 19.20 EO8_p17e25_PostGeoMx_CyCIF Patient1_B5 LSP16104.ome.tif AWS 147.00 EO4_TB_MDSC_rerun Patient1_B5 LSP16105.ome.tif AWS 164.00 EO5_B5 and AHRI samples Patient2 LSP16031.ome.tif AWS 11.30 p17_e6_TB_Granulomas_GeoMx IF HE Image Data Patient ID File Name Location File Size (GB) Patient1_B4 LSP24521.ome.tif AWS 12.15 Patient1_B4 LSP24524.ome.tif AWS 14.00 Patient1_B4 LSP24527.ome.tif AWS 13.48 Patient1_B4 LSP24530.ome.tif AWS 12.78 Patient1_B4 LSP24533.ome.tif AWS 13.78 Patient1_B4 LSP24536.ome.tif AWS 16.61 Patient1_B4 LSP24539.ome.tif AWS 16.72 Patient1_B4 LSP24542.ome.tif AWS 16.42 Patient1_B4 LSP24545.ome.tif AWS 18.33 Patient1_B4 LSP24548.ome.tif AWS 13.97 Patient1_B4 LSP24551.ome.tif AWS 12.54 Patient1_B4 LSP24554.ome.tif AWS 13.91 Patient1_B4 LSP24557.ome.tif AWS 13.83 Patient1_B4 LSP24560.ome.tif AWS 13.21 Patient1_B4 LSP24563.ome.tif AWS 13.25 Patient1_B4 LSP24566.ome.tif AWS 13.93 Patient1_B4 LSP24569.ome.tif AWS 13.46 Patient1_B4 LSP24572.ome.tif AWS 14.41 Patient1_B4 LSP24575.ome.tif AWS 13.23 Patient1_B4 LSP24578.ome.tif AWS 13.43 Patient1_B4 LSP24581.ome.tif AWS 13.23 Patient1_B4 LSP24584.ome.tif AWS 12.64 Patient1_B4 LSP24587.ome.tif AWS 13.73 Patient1_B4 LSP24590.ome.tif AWS 13.01 Patient1_B4 LSP24593.ome.tif AWS 12.73 Patient1_B4 LSP24596.ome.tif AWS 13.72 Patient1_B4 LSP24599.ome.tif AWS 17.65 Patient1_B4 LSP24602.ome.tif AWS 11.89 Patient1_B4 LSP24605.ome.tif AWS 16.95 Patient1_B4 LSP24608.ome.tif AWS 14.84 Patient1_B4 LSP24611.ome.tif AWS 13.68 Patient1_B4 LSP24614.ome.tif AWS 13.78 Patient1_B4 LSP24617.ome.tif AWS 13.49 Patient1_B4 LSP24620.ome.tif AWS 14.22 Patient1_B4 LSP24623.ome.tif AWS 13.12 Patient1_B4 LSP24626.ome.tif AWS 13.01 Patient1_B4 LSP24629.ome.tif AWS 13.53 Patient1_B4 LSP24632.ome.tif AWS 12.78 Patient1_B4 LSP24635.ome.tif AWS 13.39 Patient1_B4 LSP24638.ome.tif AWS 11.72 Patient1_B5 LSP16103.ome.tif AWS 0.84 Patient1_B5 LSP16106.ome.tiff AWS 19.70 Segmentation Mask Data Patient ID File Name Location File Size (GB) Antibody Panel Patient1_B4 LSP24522.ome.tif AWS 17.39 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24525.ome.tif AWS 16.20 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24528.ome.tif AWS 16.20 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24531.ome.tif AWS 17.39 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24534.ome.tif AWS 17.39 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24537.ome.tif AWS 16.73 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24540.ome.tif AWS 14.93 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24543.ome.tif AWS 16.73 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24546.ome.tif AWS 16.20 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24549.ome.tif AWS 17.39 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24552.ome.tif AWS 16.20 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24555.ome.tif AWS 16.84 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24558.ome.tif AWS 17.39 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24561.ome.tif AWS 17.39 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24564.ome.tif AWS 16.84 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24567.ome.tif AWS 15.57 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24570.ome.tif AWS 16.84 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24573.ome.tif AWS 18.05 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24576.ome.tif AWS 18.05 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24579.ome.tif AWS 16.20 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24582.ome.tif AWS 18.05 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24585.ome.tif AWS 16.20 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24588.ome.tif AWS 17.39 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24591.ome.tif AWS 15.57 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24594.ome.tif AWS 16.73 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24597.ome.tif AWS 16.20 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24600.ome.tif AWS 16.84 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24603.ome.tif AWS 17.39 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24606.ome.tif AWS 17.39 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24609.ome.tif AWS 18.05 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24612.ome.tif AWS 16.08 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24615.ome.tif AWS 18.18 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24618.ome.tif AWS 16.20 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24621.ome.tif AWS 16.20 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24624.ome.tif AWS 16.20 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24627.ome.tif AWS 17.39 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24630.ome.tif AWS 16.73 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24633.ome.tif AWS 15.57 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24636.ome.tif AWS 16.20 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24639.ome.tif AWS 14.93 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B5 LSP16101.ome.tif AWS 22.30 ORION imaging panel Patient1_B5 LSP16102.ome.tif AWS 0.316 EO8_p17e25_PostGeoMx_CyCIF Patient1_B5 LSP16104.ome.tif AWS 6.83 EO4_TB_MDSC_rerun Patient1_B5 LSP16105.ome.tif AWS 7.16 EO5_B5 and AHRI samples Features Table Data Patient ID File Name Location File Size (GB) Antibody Panel Patient1_B4 LSP24522.csv AWS 1.16 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24525.csv AWS 1.20 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24528.csv AWS 1.16 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24531.csv AWS 1.31 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24534.csv AWS 1.18 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24537.csv AWS 1.19 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24540.csv AWS 1.21 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24543.csv AWS 1.21 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24546.csv AWS 1.23 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24549.csv AWS 1.19 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24552.csv AWS 1.22 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24555.csv AWS 1.18 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24558.csv AWS 1.20 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24561.csv AWS 1.14 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24564.csv AWS 1.17 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24567.csv AWS 1.16 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24570.csv AWS 1.30 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24573.csv AWS 1.13 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24576.csv AWS 1.13 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24579.csv AWS 1.10 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24582.csv AWS 1.16 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24585.csv AWS 1.11 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24588.csv AWS 1.13 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24591.csv AWS 1.11 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24594.csv AWS 1.14 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24597.csv AWS 1.07 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24600.csv AWS 1.10 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24603.csv AWS 1.13 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24606.csv AWS 1.08 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24609.csv AWS 1.11 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24612.csv AWS 0.99 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24615.csv AWS 1.20 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24618.csv AWS 0.96 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24621.csv AWS 0.98 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24624.csv AWS 0.96 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24627.csv AWS 1.00 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24630.csv AWS 0.98 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24633.csv AWS 0.94 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24636.csv AWS 1.00 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B4 LSP24639.csv AWS 0.92 p17e16_EO7_B4_3D IMAGE RECONSTRUCTION Patient1_B5 LSP16101.csv AWS 0.51 ORION imaging panel Patient1_B5 LSP16102.csv AWS 1.67 EO8_p17e25_PostGeoMx_CyCIF Patient1_B5 LSP16104.csv AWS 1.71 EO4_TB_MDSC_rerun Patient1_B5 LSP16105.csv AWS 2.24 EO5_B5 and AHRI samples 3D Image Data (in Imaris Format) Patient ID File Name Location File Size (GB) Patient1_B4 Patient1_B4_3D_TLS.ims AWS 8640.00 Patient1_B4 output1.ims AWS 124.00 Patient1_B4 output2.ims AWS 72.70 Patient1_B4 output4.ims AWS 65.60 Patient1_B4 output5.ims AWS 142.00 Patient1_B4 output6.ims AWS 65.30 ADDITIONAL NOTES/COMMENTS Please contact tissue-atlas(at)hms.harvard.edu if you have any questions related to the data.
本仓库收录了与《基于三维谱分析与轨迹分析建模肺结核中三级淋巴结构（tertiary lymphoid structures, TLS）发育》相关的原始数据索引及访问指南。 # 目录 ## 基本信息 本数据集关联的研究论文标题为："Modeling development of tertiary lymphoid structures in pulmonary tuberculosis by 3D profiling and trajectory analysis"。 ### 作者 Emmanuel C. Ogbonna、Soheil R. Talemi、Zoltan Maliga、Ziyuan Zhao、Clarence Yapp、Shishir Pant、Yi Daniel Lu、Jeremy Muhlich、Andréanne Gagné、Amanda J. Martinot、Shannon Coy、Sandro Santagata、Angela Shih、Isaac H. Solomon、Threnesan Naidoo、Bree B. Aldridge、Adrie Steyn、Peter K. Sorger† ### 推荐引用格式 请按照以下格式引用本数据集： > Ogbonna 与 Rastgou Talemi（2026）. 基于三维谱分析与轨迹分析建模肺结核中三级淋巴结构发育. bioRxiv, https://doi.org/10.64898/2026.06.03.725201 ### 实用链接 关联GitHub仓库：https://github.com/labsyspharm/TB-3D-TLS-2026/ ## 文件组织方式 所有文件遵循以下命名规则：每个文件夹对应一个患者样本（记为N）。 | 文件类型 | 描述 | 存储位置 | | ---- | ---- | ---- | | `N.ome.tif` | 拼接后的多重循环免疫荧光（Cyclic Immunofluorescence, CyCIF）图像金字塔，格式为ome.tif | AWS | | `N.ome.tif` | 相邻福尔马林固定石蜡包埋（Formalin-Fixed Paraffin-Embedded, FFPE）组织切片的苏木精-伊红（Hematoxylin and Eosin, HE）染色图像 | AWS | | `N.ome.tif` | 细胞分割掩码图像 | AWS | | `N.csv` | 单细胞特征表，包含所有通道的强度数据 | AWS | | `N.fastq` | GeoMx测序数据 | 基因表达综合数据库（Gene Expression Omnibus, GEO） | | `N.ims` | 经拼接与配准的三维多重CyCIF图像，格式为.ims | AWS | ### AWS数据访问 高分辨率CyCIF图像、单细胞分割掩码及细胞计数表可通过AWS获取，所需存储桶名称为：`lsp-public-data/ogbonna-2026-tb-tls/`。 如需了解AWS数据访问指南，请访问《在AWS上访问系统药理学实验室数据集》（https://zenodo.org/records/10223574）。 若无法访问上述AWS S3存储桶，请发送邮件至 `tissue-atlas(at)hms.harvard.edu`，邮件主题为"ogbonna-2026-tb-tls: Data Access"。 ### GEO数据访问 GeoMx基因表达数据可通过基因表达综合数据库（Gene Expression Omnibus, GEO）获取，登录号为`GSE318959`。 ### 其他仓库 本研究产生的图像数据可通过盖茨结核病数据门户（https://idp.tissue-atlas.org/）获取。如需访问，请发送邮件至`tissue-atlas(at)hms.harvard.edu`，邮件主题为"Gates TB Data Portal: Data Access"。 ## 文件列表 ### CyCIF图像数据 | 患者ID | 文件名 | 存储位置 | 文件大小（GB） | 抗体组合 | | ---- | ---- | ---- | ---- | ---- | | Patient1_B4 | LSP24522.ome.tif | AWS | 222.37 | p17e16_EO7_B4_3D IMAGE RECONSTRUCTION | | Patient1_B4 | LSP24525.ome.tif | AWS | 202.51 | p17e16_EO7_B4_3D IMAGE RECONSTRUCTION | | ...（Patient1_B4剩余40条CyCIF图像文件格式一致，不再逐一列出） | ... | ... | ... | ... | | Patient1_B5 | LSP16101.ome.tif | AWS | 214.00 | ORION imaging panel | | Patient1_B5 | LSP16102_B5_Scan1.ome.tiff | AWS | 15.30 | p17_e6_TB_Granulomas_GeoMx IF | | Patient1_B5 | LSP16102.ome.tif | AWS | 19.20 | EO8_p17e25_PostGeoMx_CyCIF | | Patient1_B5 | LSP16104.ome.tif | AWS | 147.00 | EO4_TB_MDSC_rerun | | Patient1_B5 | LSP16105.ome.tif | AWS | 164.00 | EO5_B5 and AHRI samples | | Patient2 | LSP16031.ome.tif | AWS | 11.30 | p17_e6_TB_Granulomas_GeoMx IF | ### 苏木精-伊红染色图像数据 | 患者ID | 文件名 | 存储位置 | 文件大小（GB） | | ---- | ---- | ---- | ---- | | Patient1_B4 | LSP24521.ome.tif | AWS | 12.15 | | ...（Patient1_B4剩余41条HE图像文件格式一致，不再逐一列出） | ... | ... | ... | | Patient1_B5 | LSP16103.ome.tif | AWS | 0.84 | | Patient1_B5 | LSP16106.ome.tiff | AWS | 19.70 | ### 分割掩码数据 | 患者ID | 文件名 | 存储位置 | 文件大小（GB） | 抗体组合 | | ---- | ---- | ---- | ---- | ---- | | Patient1_B4 | LSP24522.ome.tif | AWS | 17.39 | p17e16_EO7_B4_3D IMAGE RECONSTRUCTION | | ...（Patient1_B4剩余41条分割掩码文件格式一致，不再逐一列出） | ... | ... | ... | ... | | Patient1_B5 | LSP16101.ome.tif | AWS | 22.30 | ORION imaging panel | | Patient1_B5 | LSP16102.ome.tif | AWS | 0.316 | EO8_p17e25_PostGeoMx_CyCIF | | Patient1_B5 | LSP16104.ome.tif | AWS | 6.83 | EO4_TB_MDSC_rerun | | Patient1_B5 | LSP16105.ome.tif | AWS | 7.16 | EO5_B5 and AHRI samples | ### 特征表数据 | 患者ID | 文件名 | 存储位置 | 文件大小（GB） | 抗体组合 | | ---- | ---- | ---- | ---- | ---- | | Patient1_B4 | LSP24522.csv | AWS | 1.16 | p17e16_EO7_B4_3D IMAGE RECONSTRUCTION | | ...（Patient1_B4剩余41条特征表文件格式一致，不再逐一列出） | ... | ... | ... | ... | | Patient1_B5 | LSP16101.csv | AWS | 0.51 | ORION imaging panel | | Patient1_B5 | LSP16102.csv | AWS | 1.67 | EO8_p17e25_PostGeoMx_CyCIF | | Patient1_B5 | LSP16104.csv | AWS | 1.71 | EO4_TB_MDSC_rerun | | Patient1_B5 | LSP16105.csv | AWS | 2.24 | EO5_B5 and AHRI samples | ### Imaris格式三维图像数据 | 患者ID | 文件名 | 存储位置 | 文件大小（GB） | | ---- | ---- | ---- | ---- | | Patient1_B4 | Patient1_B4_3D_TLS.ims | AWS | 8640.00 | | Patient1_B4 | output1.ims | AWS | 124.00 | | Patient1_B4 | output2.ims | AWS | 72.70 | | Patient1_B4 | output4.ims | AWS | 65.60 | | Patient1_B4 | output5.ims | AWS | 142.00 | | Patient1_B4 | output6.ims | AWS | 65.30 | ## 附加说明与注释 若您对本数据集有任何疑问，请联系`tissue-atlas(at)hms.harvard.edu`。
