DOI: 10.48539/hbm453.cpjp.646
title: OMAP-1 Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Lymph Node with IBEX, v1.5

description: OMAP-1 was designed for IBEX (Iterative Bleaching Extends multi-pleXity) imaging of fixed frozen human lymph nodes<br>(Radtke et al. 2020; 2022). The panel contains 39 antibodies and the nuclear marker Hoechst 33342 for image alignment<br>and nuclear segmentation. This OMAP provides a spatial context for all anatomical structures and most cell types<br>present in the ASCT+B lymph node table, v1.1 (Jorgensen, Radtke, and Rodriguez 2021). Additionally, the inclusion of<br>protein biomarkers BCL2, CD10, CD138, and CD44 allow profiling of lymph node disease states, e.g., follicular lymphoma<br>and metastasis. The core and prioritized OMAP targets detailed here overlap (~50-85%) with panels developed for<br>multiplexed imaging of lymphoid samples using other technologies and sample preparations (Lin et al. 2018;<br>Kennedy‐Darling et al. 2021). This OMAP does not contain antibodies for typing pericytes, plasmacytoid dendritic<br>cells, or different T helper lineages (Th1, Th2, Th17). Beyond spatial mapping of healthy human lymph nodes, this OMAP<br>was used to characterize the tissue microenvironment of follicular lymphoma lymph nodes. For this study, object-based<br>cellular segmentation was performed using a convolutional neural network (CNN)-based approach with Mask R-CNN<br>architecture and ResNet-50 as a backbone. As an input three channels were used: Hoechst for nuclei, CD45 as a base<br>membrane, and composite of several other membrane markers (CD138, CD163, CD94, CD69, CD8, CD4). More details and<br>accompanying datasets associated with OMAP-1 can be found here (Radtke et al. 2024; Andrea J Radtke et al. 2021).<br>Several antibodies required custom conjugation by commercial suppliers or antibody conjugation kits (e.g., Alexa Fluor<br>532, Thermo Fisher Scientific A20182). Additional details on the IBEX method, sample preparation, reagent validation,<br>and example datasets can be found on the IBEX Knowledge-Base (Radtke et al. 2025, Yaniv et al. 2025).<br><br>**Bibliography:**<br><br>* Andrea J Radtke, Colin J Chu, Ziv Yaniv, Li Yao, James Marr, Rebecca T Beuschel, Hiroshi Ichise, et al. 2021. “Accompanying Dataset for: ‘IBEX: An Iterative Immunolabeling and Chemical Bleaching Method for High-Content Imaging of Diverse Tissues.’” Zenodo. https://zenodo.org/records/5244551.<br>* Jorgensen, Marda, Andreas Radtke, and Natalie Rodriguez. 2021. “Lymph-Node (v1.1) Graph Data, v1.1.” 2021. https://lod.humanatlas.io/asct-b/lymph-node/v1.1/.<br>* Kennedy‐Darling, Julia, Salil S. Bhate, John W. Hickey, Sarah Black, Graham L. Barlow, Gustavo Vazquez, Vishal G. Venkataraaman, et al. 2021. “Highly Multiplexed Tissue Imaging Using Repeated Oligonucleotide Exchange Reaction.” *European Journal of Immunology* 51 (5): 1262–77. https://doi.org/10.1002/eji.202048891.<br>* Lin, Jia-Ren, Benjamin Izar, Shu Wang, Clarence Yapp, Shaolin Mei, Parin M Shah, Sandro Santagata, and Peter K Sorger. 2018. “Highly Multiplexed Immunofluorescence Imaging of Human Tissues and Tumors Using T-CyCIF and Conventional Optical Microscopes.” *eLife* 7 (July): e31657. https://doi.org/10.7554/eLife.31657.<br>* Radtke, Andrea J., Colin J. Chu, Ziv Yaniv, Li Yao, James Marr, Rebecca T. Beuschel, Hiroshi Ichise, et al. 2022. “IBEX: An Iterative Immunolabeling and Chemical Bleaching Method for High-Content Imaging of Diverse Tissues.” *Nature Protocols* 17 (2): 378–401. https://doi.org/10.1038/s41596-021-00644-9.<br>* Radtke, Andrea J., Evelyn Kandov, Bradley Lowekamp, Emily Speranza, Colin J. Chu, Anita Gola, Nishant Thakur, et al. 2020. “IBEX: A Versatile Multiplex Optical Imaging Approach for Deep Phenotyping and Spatial Analysis of Cells in Complex Tissues.” *Proceedings of the National Academy of Sciences* 117 (52): 33455–65. https://doi.org/10.1073/pnas.2018488117.<br>* Radtke, Andrea J., Ekaterina Postovalova, Arina Varlamova, Alexander Bagaev, Maria Sorokina, Olga Kudryashova, Mark Meerson, et al. 2024. “Multi-Omic Profiling of Follicular Lymphoma Reveals Changes in Tissue Architecture and Enhanced Stromal Remodeling in High-Risk Patients.” *Cancer Cell* 42 (3): 444–463.e10. https://doi.org/10.1016/j.ccell.2024.02.001.<br>* Radtke, Andrea J., Ifeanyichukwu U. Anidi, Leanne Arakkal, Armando J Arroyo-Mejías, Rebecca T. Beuschel, Katy Börner, Colin J. Chu, et al. 2025. “The IBEX Knowledge-Base: A Central Resource for Multiplexed Imaging Techniques.” *PLOS Biology* 23 (3): e3003070. https://doi.org/10.1371/journal.pbio.3003070.<br>* Yaniv, Ziv, Ifeanyichukwu U. Anidi, Leanne Arakkal, Armando J Arroyo-Mejías, Rebecca T. Beuschel, Katy Börner, Colin J. Chu, et al. 2025. “The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluorescence Imaging Methods.” *eLife* 14: RP105737.