Highly Multiplexed 3D Profiling of Cell States and Immune Niches in Human Tumours

This respository hosts original code associated with "Highly Multiplexed 3D Profiling of Cell States and Immune Niches in Human Tumours". This includes 3D image registration, intensity quantification, cell shape & orientation analysis, collagen-to-cell distance quantification, and cell interaction analysis. See Data Access section for instructions on accessing the primary data associated with this paper. TABLE OF CONTENTS GENERAL INFORMATION TITLE AUTHORS AND BEST CONTACT LICENSES USEFUL LINKS FILE ORGANIZATION FILE TYPES DATA ACCESS FILE LIST ---- GENERAL INFORMATION Publication: Highly Multiplexed 3D Profiling of Cell States and Immune Niches in Human Tumours. [Forthcoming]. Authors: Clarence Yapp, Ajit J. Nirmal, Felix Zhou, Alex Y.H. Wong, Juliann B. Tefft, Yi Daniel Lu, Zhiguo Shang, Zoltan Maliga, Paula Montero Llopis, George F. Murphy, Christine G. Lian, Gaudenz Danuser, Sandro Santagata, and Peter K. Sorger Contact Information: tissue-atlas(at)hms.harvard.edu or Peter Sorger; peter_sorger(at)hms.harvard.edu Licenses/restrictions placed on the data: CC-BY creativecommons.org/licenses/by/4.0/ Useful links: Preprint Publication: https://www.biorxiv.org/content/10.1101/2023.11.10.566670v4 Associated GitHub Repository: labsyspharm/mel-3d-mis To view the image data online, visit: https://www.tissue-atlas.org/atlas-datasets/yapp-nirmal-2023 ---- FILE ORGANIZATION FILE TYPES Stitched and registered 3D multiplexed data is available for download through AWS. File Type Description Location N.ims Stitched and registered 3D multiplexed CyCIF image pyramid in .ims format AWS DATA ACCESS AWS Data Access: s3://lsp-public-data/yapp-2023-3d-melanoma/ Visit the following Zenodo page for instructions on how to access primary image data associated with this publication: Access Laboratory of Systems Pharmacology Datasets on AWS, DOI: 10.5281/zenodo.10223574 Contact: If you experience issues accessing the above AWS S3 buckets, email tissue-atlas(at)hms.harvard.edu with the subject line "s3://lsp-public-data/yapp-2023-3d-melanoma/: Data Access". FILE LIST LSP Slide ID File Name File Size (GB) LSP13626 Dataset1-LSP13626-invasive-margin.ims 935 LSP13626 Dataset1-LSP13626-melanoma-in-situ.ims 340 LSP13625 Dataset2-LSP13625-invasive-margin.ims 94 LSP13625 Dataset2-LSP13625-melanoma-in-situ.ims 103 LSP22409 Dataset2-LSP13625-melanoma-in-situ.im 614 LSP13357 LSP13357.ims 145 LSP17378 LSP17378.ims 385 LSP18251 LSP18251_TR3.ims 205 LSP18251 LSP18251_TR4.ims 288 LSP18251 LSP18251_TR5.ims 134 LSP22408 LSP22408.ims 2.5 3245.5