Deep profiling of mouse splenic architecture with CODEX multiplexed imaging

Cited by (1,001)

Items 601–700 of 1,001

1. Temporal tissue dynamics from a spatial snapshot
   Jonathan Somer, Shie Mannor, Uri Alon · 2026 · Nature
2. Flexible Cyclic Immunofluorescence (cyCIF) Using Oligonucleotide Barcoded Antibodies
   Nathan P. McMahon, Jocelyn A. Jones, Ashley N. Anderson, Matthew S. Dietz, Melissa Hirose Wong, Summer L. Gibbs · 2023 · Cancers
3. Human resident liver myeloid cells protect against metabolic stress in obesity
   Emelie Barreby, Benedikt Strunz, Sebastian Nock, Léa Naudet, Joanne X. Shen, Helene Johansson, Isabella Sönnerborg, Junjie Ma, Egon Urgard, Laura J. Pallett et al. · 2023 · Nature Metabolism
4. Bioengineering translational models of lymphoid tissues
   Yale S. Michaels, Cara F. Buchanan, Nikolche Gjorevski, Annie Moisan · 2023 · Nature Reviews Bioengineering
5. Delineating spatial cell-cell interactions in the solid tumour microenvironment through the lens of highly multiplexed imaging
   David E. Cohn, Aisling Forder, Erin A. Marshall, Emily A. Vucic, Greg L. Stewart, Kouther Noureddine, William Wirt Lockwood, Calum E. MacAulay, Martial D. Guillaud, Wan L. Lam · 2023 · Frontiers in Immunology
6. Cellstitch: 3D cellular anisotropic image segmentation via optimal transport
   Yining Liu, Yinuo Jin, Elham Azizi, Andrew J. Blumberg · 2023 · BMC Bioinformatics
7. Multiplex imaging of localized prostate tumors reveals altered spatial organization of AR-positive cells in the microenvironment
   Çiğdem Ak, Zeynep Sayar, Guillaume Thibault, Erik A. Burlingame, Marigold Kuykendall, Jennifer R. Eng, Alex Chitsazan, Koei Chin, Andrew Adey, Christopher T. Boniface et al. · 2024 · iScience
8. Basal-to-inflammatory transition and tumor resistance via crosstalk with a pro-inflammatory stromal niche
   Nancy Yanzhe Li, Weiruo Zhang, Daniel Haensel, Anna R. Jussila, Cory Pan, Sadhana Gaddam, Sylvia K. Plevritis, Anthony E. Oro · 2024 · Nature Communications
9. PENGUIN: A rapid and efficient image preprocessing tool for multiplexed spatial proteomics
   Ana Marta Sequeira, Marieke E. Ijsselsteijn, Miguel Rocha, Noel F.C.C. de Miranda · 2024 · Computational and Structural Biotechnology Journal
10. Understanding CLL biology through mouse models of human genetics
    Elisa ten Hacken, Catherine J. Wu · 2021 · Blood
11. Cyclic microchip assay for measurement of hundreds of functional proteins in single neurons
    Liwei Yang, Avery Ball, Jesse J. Liu, Tanya Jain, Yue‐Ming Li, Firoz Akhter, Donghui Zhu, Jun Wang · 2022 · Nature Communications
12. Griottes: a generalist tool for network generation from segmented tissue images
    Gustave Ronteix, Andrey I. Aristov, Valentin Bonnet, Sébastien Sart, Jeremie Sobel, Elric Esposito, Charles Naim Baroud · 2022 · BMC Biology
13. Multicellular modules as clinical diagnostic and therapeutic targets
    Marc‐Andrea Baertsch, Garry P. Nolan, John W. Hickey · 2021 · Trends in cancer
14. High Resolution Single Cell Maps Reveals Distinct Cell Organization and Function Across Different Regions of the Human Intestine
    John W. Hickey, Winston R. Becker, Stephanie A. Nevins, Aaron M. Horning, Almudena Espín-Pérez, Roxanne Chiu, Derek C. Chen, Daniel J. Cotter, Edward D. Esplin, Annika K K Weimer et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
15. Precision Medicine in Pancreatic Disease—Knowledge Gaps and Research Opportunities: Summary of a National Institute of Diabetes and Digestive and Kidney Diseases Workshop
    Lowe, Mark E., Andersen, Dana K., Caprioli, Richard M., Choudhary, Jyoti, Cruz-Monserrate, Zobeida, Dasyam, Anil K., Forsmark, Christopher E., Gorelick, Fred S., Gray, Joe W., Haupt, Mark et al. · 2019 · Pancreas
16. The burgeoning spatial multi-omics in human gastrointestinal cancers
    Weizheng Liang, Zhenpeng Zhu, Dandan Xu, Peng Wang, Fei Guo, Haoshan Xiao, Chenyang Hou, Jun Wu Xue, Xuejun Zhi, Rensen Ran · 2024 · PeerJ
17. Exploring Multiplex Immunohistochemistry ( mIHC ) Techniques and Histopathology Image Analysis: Current Practice and Potential for Clinical Incorporation
    Aria Kaiyuan Sun, Song Fan, S. W. Choi · 2025 · Cancer Medicine
18. Learning tissue representation by identification of persistent local patterns in spatial omics data
    Jovan Tanevski, Loan Vulliard, Miguel A. Ibarra-Arellano, Denis Schapiro, Felix J. Hartmann, Julio Sáez-Rodríguez · 2025 · Nature Communications
19. CellLENS enables cross-domain information fusion for enhanced cell population delineation in single-cell spatial omics data
    Bokai Zhu, Sheng Gao, Shuxiao Chen, Yuchen Wang, Jason Yeung, Yunhao Bai, Amy Y. Huang, Yao Yu Yeo, Guanrui Liao, Shulin Mao et al. · 2025 · Nature Immunology
20. iPEX enables micrometre-resolution deep spatial proteomics via tissue expansion
    Fengxiang Wang, Cuiji Sun, Tianshu William Wu, Yuting Fu, Yujing Fan, Shuchang Zhao, Kaiyin Huang, Zijian Pan, Lu Yang, Jingrong Regina Han et al. · 2025 · Nature
21. Bridging the dimensional gap from planar spatial transcriptomics to 3D cell atlases
    Senlin Lin, Zhikang Wang, Yan Cui, Qi Zou, Chuangyi Han, Rui Yan, Zhidong Yang, Wei Zhang, Rui Gao, Jiangning Song et al. · 2025 · Nature Methods
22. Single-cell spatial pharmacobiology identifies conserved stromal barriers to therapeutic antibody delivery in human solid tumors
    Guolan Lu, John W. Hickey, Maximilian Haist, Xulei Qin, Dr. Emily Zhao, Abdullah Naveed, Erna Forgó, Marc‐Andrea Baertsch, Lucas Mani, Xavier Rovira‐Clavé et al. · 2026 · Nature Biotechnology
23. The MEMIC is an ex vivo system to model the complexity of the tumor microenvironment
    Libuše Janská, Libi Anandi V, Nell C. Kirchberger, Zoran S. Marinkovic, Logan T. Schachtner, Gizem Guzelsoy, Carlos Carmona‐Fontaine · 2021 · Disease Models & Mechanisms
24. Achieving a Deeper Understanding of Drug Metabolism and Responses Using Single-Cell Technologies
    Abigail M. Wheeler, Colten D. Eberhard, Eric P. Mosher, Yuting Yuan, Hannah N. Wilkins, Herana Kamal Seneviratne, Benjamin C. Orsburn, Namandjé N. Bumpus · 2023 · Drug Metabolism and Disposition
25. Computational Methods for Single-Cell Proteomics
    Sophia M. Guldberg, Trine Line Hauge Okholm, Elizabeth E. McCarthy, Matthew H. Spitzer · 2023 · Annual Review of Biomedical Data Science
26. Deriving spatial features from in situ proteomics imaging to enhance cancer survival analysis
    Monica T. Dayao, Alexandro E. Trevino, Honesty Kim, Matthew Ruffalo, H. Blaize D’Angio, Ryan Preska, Umamaheswar Duvvuri, Aaron T. Mayer, Ziv Bar‐Joseph · 2023 · Bioinformatics
27. Cyclone: an accessible pipeline to analyze, evaluate, and optimize multiparametric cytometry data
    Ravi K. Patel, Rebecca Garrett Jaszczak, Kwok Wai Im, Nicholas D. Carey, Tristan Courau, Daniel G. Bunis, Bushra Samad, Lia Avanesyan, Nayvin W. Chew, Sarah Stenske et al. · 2023 · Frontiers in Immunology
28. Recent methodological advances towards single-cell proteomics
    Sooyeon Kim, Latiefa Kamarulzaman, Yuichi Taniguchi · 2023 · Proceedings of the Japan Academy Series B
29. SpaceANOVA: Spatial Co-occurrence Analysis of Cell Types in Multiplex Imaging Data Using Point Process and Functional ANOVA
    Souvik Seal, Brian Neelon, Peggi M. Angel, Elizabeth C. O’Quinn, Elizabeth Goodwin Hill, Thao Vu, Debashis Ghosh, Anand S. Mehta, Kristin Wallace, Alexander V. Alekseyenko · 2024 · Journal of Proteome Research
30. scBOL: a universal cell type identification framework for single-cell and spatial transcriptomics data
    Yuyao Zhai, Liang Chen, Minghua Deng · 2024 · Briefings in Bioinformatics
31. A versatile tissue-rolling technique for spatial-omics analyses of the entire murine gastrointestinal tract
    Gustavo Monasterio, Rodrigo A. Morales, David Alejandro Bejarano, Xesús Manoel Abalo, Jennifer Fransson, Ludvig Larsson, Andreas Schlitzer, Joakim Lundeberg, Srustidhar Das, Eduardo J. Villablanca · 2024 · Nature Protocols
32. The Society for Immunotherapy of Cancer Perspective on Tissue-Based Technologies for Immuno-Oncology Biomarker Discovery and Application
    Anne Monette, Adriana Aguilar‐Mahecha, Emre Altınmakas, Mathew G. Angelos, Nima Assad, Gerald Batist, Praveen K. Bommareddy, Diana Lucia Bonilla, Christoph H. Borchers, SE Church et al. · 2024 · Clinical Cancer Research
33. Characterizing cell-type spatial relationships across length scales in spatially resolved omics data
    Rafael dos Santos Peixoto, Brendan F. Miller, Maigan Brusko, Gohta Aihara, Lyla Atta, Manjari M-G Anant, Mark A. Atkinson, Todd M. Brusko, Clive Henry Wasserfall, Jean Fan · 2025 · Nature Communications
34. Advances in tissue-based imaging: impact on oncology research and clinical practice
    Arman Rahman, Chowdhury Arif Jahangir, Seodhna M. Lynch, Nebras Al-Attar, Claudia Monica Aura, Niamh M. Russell, Fiona T. Lanigan, William M. Gallagher · 2020 · Expert Review of Molecular Diagnostics
35. SYLARAS: A Platform for the Statistical Analysis and Visual Display of Systemic Immunoprofiling Data and Its Application to Glioblastoma
    Gregory J. Baker, Jeremy L. Muhlich, Sucheendra K. Palaniappan, Jodene K. Moore, Stephanie H. Davis, Sandro Santagata, Peter Karl Sorger · 2020 · Cell Systems
36. Immune Monitoring for Advanced Cell Therapy Trials in Transplantation: Which Assays and When?
    Helen L. Stark, Chenyu Wang, Jasmina Kuburic, Alaa Alzhrani, Joanna Hester, Fadi Issa · 2021 · Frontiers in Immunology
37. Histological Studies of the Ventricular–Subventricular Zone as Neural Stem Cell and Glioma Stem Cell Niche
    Asa A. Brockman, B. Mobley, Rebecca A. Ihrie · 2021 · Journal of Histochemistry and Cytochemistry
38. User-Accessible Machine Learning Approaches for Cell Segmentation and Analysis in Tissue
    Seth Winfree · 2022 · Frontiers in Physiology
39. Isolating and cryopreserving pig skin cells for single-cell RNA sequencing study
    Li Han, Carlos Poblete Jara, Ou Wang, Yu Shi, Xinran Wu, Sandra Thibivilliers, Rafał Kazimierz Wóycicki, Mark A. Carlson, William H. Velander, ELIANA PEREIRA DE ARAUJO et al. · 2022 · PLoS ONE
40. DenVar: density-based variation analysis of multiplex imaging data
    Souvik Seal, Thao Vu, Tusharkanti Ghosh, Julia Wrobel, Debashis Ghosh · 2022 · Bioinformatics Advances
41. Tyramide-conjugated DNA barcodes enable signal amplification for multiparametric CODEX imaging
    Paul D. Simonson, Itzel Valencia, Sanjay S. Patel · 2022 · Communications Biology
42. FunSpace: A functional and spatial analytic approach to cell imaging data using entropy measures
    Thao Vu, Souvik Seal, Julia Wrobel, Tusharkanti Ghosh, Mansooreh Ahmadian, Debashis Ghosh · 2023 · PLoS Computational Biology
43. Decoding the body language of immunity: Tackling the immune system at the organism level
    Nicolas Chevrier · 2019 · Current Opinion in Systems Biology
44. Single-cell analyses uncover granularity of muscle stem cells
    John Saber, Alexander Y. Lin, Michael A. Rudnicki · 2020 · F1000Research
45. Highly Sensitive and Multiplexed In-Situ Protein Profiling with Cleavable Fluorescent Streptavidin
    Renjie Liao, Thai H. Pham, Diego Mastroeni, Paul D. Coleman, Joshua LaBaer, Jia Guo · 2020 · Cells
46. Expanding the Scope of Antibody Rebridging with New Pyridazinedione–TCO Constructs
    Angela N. Marquard, Jonathan Carlson, Ralph Weissleder · 2020 · Bioconjugate Chemistry
47. Multiplex Spatial Bioimaging for Combination Therapy Design
    Shuangyi Cai, Mayar Allam, Ahmet F. Coskun · 2020 · Trends in cancer
48. Cancer microenvironment and genomics: evolution in process
    Stanley P. L. Leong, Isaac P. Witz, Orit Sagi‐Assif, Sivan Izraely, Jonathan Paul Sleeman, Brian Piening, Bernard A. Fox, Carlo Bruno Bifulco, Rachel N. Martini, Lisa A. Newman et al. · 2021 · Clinical & Experimental Metastasis
49. Anatomy of Hematopoiesis and Local Microenvironments in the Bone Marrow. Where to?
    Qingqing Wu, Jizhou Zhang, Daniel Lucas · 2021 · Frontiers in Immunology
50. ClusterMap: multi-scale clustering analysis of spatial gene expression
    Yichun He, Xin Tang, Jiahao Huang, Haowen Zhou, Kevin Z. Chen, Albert Liu, Jingyi Ren, Hailing Shi, Zuwan Lin, Qiang Li et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
51. Spatial Patterning Analysis of Cellular Ensembles (SPACE) finds complex spatial organization at the cell and tissue levels
    Edward C. Schrom, Erin McCaffrey, Vivek Sreejithkumar, Andrea J. Radtke, Hiroshi Ichise, Armando Arroyo-Mejías, Emily E. Speranza, Leanne Arakkal, Nishant Thakur, Spencer M. Grant et al. · 2025 · Proceedings of the National Academy of Sciences
52. Bridging single cells to organs: Mesoscale modules as fundamental units of tissue function
    Yun Chen, Ronald N. Germain, Ginger L. Hunter, Rajan P. Kulkarni, Arthur D. Lander, Pedro Ricardo Lowenstein, Jeremy E. Purvis, Harikesh S. Wong · 2025 · Cell
53. Smart spatial omics (S2-omics) optimizes region of interest selection to capture molecular heterogeneity in diverse tissues
    Musu Yuan, Kaidi Jin, Hanying Yan, Amelia R. Schroeder, Chunyu Luo, Sicong Yao, Bernhard Dumoulin, Jonathan L. Levinsohn, Tianhao Luo, Jean Rene V. Clemenceau et al. · 2025 · Nature Cell Biology
54. Single‐Cell and Spatial Omics: Methods and Applications
    Xiaoping Cen, Xiaolan Huang, Erle Deng, Xue Gong, Na Tan, J. T. Ye, Yin Wang, Roland Eils, Qun Luo, Yixue Li et al. · 2026 · MedComm
55. Applicability of Spatial Technology in Cancer Research
    Seonghoon Ahn, Hye Seung Lee · 2024 · Cancer Research and Treatment
56. Steroids-producing nodules: a two-layered adrenocortical nodular structure as a precursor lesion of cortisol-producing adenoma
    Tazuru Fukumoto, Hironobu Umakoshi, Norifusa Iwahashi, Tatsuki Ogasawara, Maki Yokomoto‐Umakoshi, Hiroki Kaneko, Masamichi Fujita, Naohiro Uchida, Hiroshi Nakao, Namiko Kawamura et al. · 2024 · EBioMedicine
57. MIM-CyCIF: masked imaging modeling for enhancing cyclic immunofluorescence (CyCIF) with panel reduction and imputation
    Zachary Sims, Gordon Brent Mills, Young Hwan Chang · 2024 · Communications Biology
58. The broken Alzheimer’s disease genome
    Cláudio Gouveia Roque, Hemali P. Phatnani, Ulrich Hengst · 2024 · Cell Genomics
59. Points2Regions : Fast, interactive clustering of imaging‐based spatial transcriptomics data
    Axel Andersson, Andrea Beháňová, Christophe Avenel, Jonas Windhager, Filip Malmberg, Carolina Wählby · 2024 · Cytometry Part A
60. Cinco de Bio: A Low-Code Platform for Domain-Specific Workflows for Biomedical Imaging Research
    Colm Brandon, Steve Boßelmann, Amandeep Singh, Stephen Ryan, Alexander Schieweck, Éanna Fennell, Bernhard Steffen, Tiziana Margaria · 2024 · BioMedInformatics
61. Segmentation aware probabilistic phenotyping of single-cell spatial protein expression data
    Yu‐Ju Lee, Edward L.Y. Chen, Darren C. H. Chan, Anuroopa Dinesh, Somaieh Afiuni‐Zadeh, Conor Klamann, Alina Selega, Miralem Mrkonjic, Hartland Warren Jackson, Kieran R. Campbell · 2025 · Nature Communications
62. Decoding Extracellular Protein Glycosylation in Human Health and Disease
    Alexandra D. Steigmeyer, Sarah Lowery, Valentina Rangel-Angarita, Stacy Alyse Malaker · 2025 · Annual Review of Analytical Chemistry
63. Immune checkpoint inhibitors plus debulking surgery for patients with metastatic renal cell carcinoma: clinical outcomes and immunological correlates of a prospective pilot trial
    Sangeeta Goswami, Jianjun Gao, Sreyashi Basu, Daniel D. Shapiro, Jose Antonio Karam, Rebecca S. Slack Tidwell, Kamran Ahrar, Matthew T. Campbell, Yu Shen, Alexandro E. Trevino et al. · 2025 · Nature Communications
64. High-dimensional imaging using combinatorial channel multiplexing and deep learning
    Raz Ben-Uri, Lior Ben Shabat, Dana Shainshein, Omer Bar-Tal, Yuval Bussi, Noa Maimon, Tal Keidar Haran, Idan Milo, Inna Goliand, Yoseph Addadi et al. · 2025 · Nature Biotechnology
65. The extra-islet pancreas supports autoimmunity in human type 1 diabetes
    Graham L. Barlow, Christian M. Schürch, Salil S. Bhate, Darci J. Phillips, Arabella Young, Shen Dong, HA. Martinez, Gernot Kaber, Nadine Nagy, S. Ramachandran et al. · 2025 · eLife
66. Proteoform profiling of endogenous single cells from rat hippocampus at scale
    Pei Su, Michael A. R. Hollas, Indira Plá, Stanislav S. Rubakhin, Fatma Ayaloglu Butun, Joseph B. Greer, Bryan P. Early, Ryan T. Fellers, Michael A. Caldwell, Jonathan V. Sweedler et al. · 2025 · Nature Biotechnology
67. The Power of Systems Biology
    Andrea Fava, Soumya Raychaudhuri, Deepak A. Rao · 2021 · Rheumatic Disease Clinics of North America
68. Ultra‐fast Cycling for Multiplexed Cellular Fluorescence Imaging
    Jina Ko, Juhyun Oh, Maaz S. Ahmed, Jonathan Carlson, Ralph Weissleder · 2020 · Angewandte Chemie
69. The localization of molecularly distinct microglia populations to Alzheimer's disease pathologies using QUIVER
    Ryan K. Shahidehpour, Abraham S. Nelson, Lydia G. Sanders, Chloe R. Embry, Peter T. Nelson, Adam D. Bachstetter · 2023 · Acta Neuropathologica Communications
70. Rhesus Macaque CODEX Multiplexed Immunohistochemistry Panel for Studying Immune Responses During Ebola Infection
    Sizun Jiang, Nilanjan Mukherjee, Richard S. Bennett, Han M. Chen, James Logue, Bonnie Dighero-Kemp, Jonathan R. Kurtz, Ricky D. Adams, Darci J. Phillips, Christian M. Schürch et al. · 2021 · Frontiers in Immunology
71. Advancing Stem Cell Research through Multimodal Single-Cell Analysis
    Iwo Kuciński, Berthold Göttgens · 2020 · Cold Spring Harbor Perspectives in Biology
72. Online narrative guides for illuminating tissue atlas data and digital pathology images
    Rumana Rashid, Yu-An Chen, John Hoffer, Jeremy L. Muhlich, Jia‐Ren Lin, Robert Krueger, Hanspeter Pfister, Richard N. Mitchell, Sandro Santagata, Peter Karl Sorger · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
73. A platform for multimodal in vivo pooled genetic screens reveals regulators of liver function
    Reuben A. Saunders, William E. Allen, Xingjie Pan, Jaspreet Sandhu, Jiaqi Lu, Thomas K. Lau, Karina Smolyar, Zuri A. Sullivan, Catherine G. Dulac, Jonathan S. Weissman et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
74. Decoding metastatic microenvironments through single-cell omics reveals new insights into niche dynamics and tumor evolution
    Fengshuo Liu, Xiang H.-F. Zhang · 2025 · PLoS Biology
75. An integrated approach for analyzing spatially resolved multi-omics datasets from the same tissue section
    Thao Phuong Tran, Felicia Yu Ting Wee, Craig Ryan Joseph, Wanqiu Zhang, Jeffrey Chun Tatt Lim, Zhen Wei Neo, Li Yen Chong, Francis Hong Xin Yap, Nathan Heath Patterson, Marc Claesen et al. · 2025 · Frontiers in Molecular Biosciences
76. Spatiotemporal Dynamics of Central Nervous System Diseases: Advancing Translational Neuropathology via Single‐Cell and Spatial Multiomics
    Mingkai Xia, Quan Liu, Wenli Zhang, Jinwen Ge, Zhigang Mei · 2025 · MedComm
77. Organ‐on‐a‐Chip Technology and Global Multi‐Omics: Current Applications and Future Directions
    Xuxia Cao, Congmin Xia, Caifeng Li, Shiwen Deng, Junxian Cao, Hongjun Yang, Shaoping Wang, Peng Chen · 2026 · MedComm
78. Spatial transcriptomics in human skin research
    Stavroula Tekkela, Georgios Theocharidis, John Alexander McGrath, Alexandros Onoufriadis · 2023 · Experimental Dermatology
79. Tissue niches and immunopathology through the lens of spatial tissue profiling techniques
    Anna Pascual Reguant, Sandy Kroh, Anja Erika Hauser · 2023 · European Journal of Immunology
80. Recent Advancements in Subcellular Proteomics: Growing Impact of Organellar Protein Niches on the Understanding of Cell Biology
    Vanya Bhushan, Aleksandra Nita‐Lazar · 2024 · Journal of Proteome Research
81. Identifying the Spatial Architecture That Restricts the Proximity of CD8+ T Cells to Tumor Cells in Pancreatic Ductal Adenocarcinoma
    Yihan Xia, Junrui Ma, Xiaobao Yang, Danping Liu, Yujie Zhu, Yanan Zhao, Xuefeng Fei, Dakang Xu, Jing Dai · 2024 · Cancers
82. Multiplex Imaging for Cell Phenotyping of Early Human Atherosclerosis
    Maria Elishaev, Boaz Li, Annie Zhou, Kevin Salim, Nicholas James Leeper, Gordon A. Francis, Chi Peng Timothy Lai, Ying Wang · 2024 · Journal of the American Heart Association
83. Discovery and generalization of tissue structures from spatial omics data
    Zhenqin Wu, Ayano Kondo, Monee McGrady, Ethan A. G. Baker, Benjamin Chidester, Eric Wu, Maha K. Rahim, Nathan A. Bracey, Vivek Charu, Raymond Jaihyun Cho et al. · 2024 · Cell Reports Methods
84. From surfing to diving into the tumor microenvironment through multiparametric imaging mass cytometry
    Marco Erreni, Maria Rita Fumagalli, M Marozzi, Roberto Leone, Raffaella Parente, Raffaella D’Anna, Andrea Doni · 2025 · Frontiers in Immunology
85. Spatial analysis identifies DC niches as predictors of pembrolizumab therapy in head and neck squamous cell cancer
    Juhyun Oh, Jan Hoelzl, Jonathan C. T. Carlson, Ruben Bill, Hannah M. Peterson, W. Faquin, M. Pittet, Sara I. Pai, R. Weissleder · 2025 · Cell Reports Medicine
86. SPEX: A modular end-to-end platform for high-plex tissue spatial omics analysis
    Xiao Li, Ximo Pechuan-Jorge, Tyler Risom, Conrad Foo, Alexander Prilipko, Artem Zubkov, Caleb K. Chan, Patrick S. Chang, Frank Peale, James M. Ziai et al. · 2025 · GigaScience
87. Deciphering the Immune Complexity in Esophageal Adenocarcinoma and Pre-Cancerous Lesions With Sequential Multiplex Immunohistochemistry and Sparse Subspace Clustering Approach
    Srinand Sundaram, Eun Na Kim, G.M. Jones, Shamilene Sivagnanam, Monika Tripathi, Ahmad Miremadi, Massimiliano di Pietro, Lisa M. Coussens, Rebecca Claire Fitzgerald, Young Hwan Chang et al. · 2022 · Frontiers in Immunology
88. Dissecting intratumor heterogeneity in HCC: new research strategies and clinical implications
    Shay Behrens, Xin Wei Wang · 2022 · Carcinogenesis
89. BLEACH&STAIN 15-marker Multiplexed Imaging in 3,098 Human Carcinomas Reveals Six Major PD-L1–driven Immune Phenotypes with Distinct Spatial Orchestration
    Elena Bady, Katharina Möller, Tim Mandelkow, Jonas B. Raedler, Cheng Hsun Yang, Julia Ebner, Magalie C.J. Lurati, Ronald Simon, Eik Vettorazzi, Franziska Büscheck et al. · 2023 · Molecular Cancer Research
90. Breast cancers as ecosystems: a metabolic perspective
    Flavia Martino, Mariadomenica Lupi, Enrico Giraudo, Letizia Lanzetti · 2023 · Cellular and Molecular Life Sciences
91. Spatial Single Cell Analysis of Proteins in 2D Human Gastruloids Using Iterative Immunofluorescence
    Emily Freeburne, Seth Teague, Hina Khan, Bolin Li, Siyuan Ding, Bohan Chen, Adam S. Helms, Idse Heemskerk · 2023 · Current Protocols
92. Viv: Multiscale Visualization of High-Resolution Multiplexed Bioimaging Data on the Web
    Trevor Manz, Ilan Gold, Nathan Heath Patterson, Chuck McCallum, Mark S. Keller, Bruce W. Herr, Katy Börner, Jeffrey M. Spraggins, Nils Gehlenborg · 2020
93. Generalized cell phenotyping for spatial proteomics with language-informed vision models
    Xuefei Wang, Rohit Dilip, Ahamed Raffey Iqbal, Yuval Bussi, Caitlin Brown, Elora Pradhan, Yashvardhan Jain, Kevin Yu, Shenyi Li, Martin Abt et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
94. Same-Slide Spatial Multi-Omics Integration Reveals Tumor Virus-Linked Spatial Reorganization of the Tumor Microenvironment
    Yao Yu Yeo, Yuzhou Chang, Huaying Qiu, Stephanie Pei Tung Yiu, Hendrik A. Michel, Wenrui Wu, Xiaojie Jin, Shoko Kure, Lindsay K. Parmelee, Shuli Luo et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
95. Oncogenic and tumor-suppressive forces converge on a progenitor niche at the benign-to-malignant transition
    Jose Reyes, Isabella S. Del Priore, Andrea C. Chaikovsky, Nikhita Pasnuri, Ahmed M. Elhossiny, Jin Park, Philipp Weiler, Tobias Krause, Andrew R Moorman, Catherine Snopkowski et al. · 2026 · Cell
96. Cellular architecture and neighborhood-informed virtual spatial tumor profiling from histopathology
    Y J. Li, Zhe Li, Ryan J. Quinton, Yuanfeng Ji, Xiaoming Zhang, Jinxi Xiang, Xiyue Wang, Sen Yang, Feyisope R. Eweje, Yijiang M. Chen et al. · 2026 · Cell
97. Ultrasensitive and Multiplexed Protein Imaging with Cleavable Fluorescent Tyramide and Antibody Stripping
    Thai H. Pham, Christopher D. Nazaroff, Joshua LaBaer, Jia Guo · 2021 · International Journal of Molecular Sciences
98. New-generation technologies for spatial tissue analysis, indispensable tools for deciphering intratumor heterogeneity in the development of antibody-drug conjugates and radio-immunoconjugates for cancer treatment
    Nina Radosevic‐Robin, Myriam Kossaï, Frederique Madeleine Penault-Llorca · 2023 · Translational Breast Cancer Research
99. Mosaic-PICASSO: accurate crosstalk removal for multiplex fluorescence imaging
    Hu Cang, Yang Liu, Jianhua Xing · 2023 · Bioinformatics
100. High-dimensional comparison of monocytes and T cells in post-COVID and idiopathic pulmonary fibrosis
     Grace C. Bingham, Lyndsey M. Muehling, Chaofan Li, Yong Huang, Shwu‐Fan Ma, Daniel Abebayehu, Imre Noth, Jie Sun, Judith A. Woodfolk, Thomas Harrison Barker et al. · 2024 · Frontiers in Immunology