Multimodal whole slide image processing pipeline for quantitative mapping of tissue architecture and tissue microenvironment
Abstract Multi-modal, multiscale imaging is crucial for quantitative high-content spatial profiling. We present an integrated image processing pipeline for comprehensive tissue analysis that combines quantitative phase microscopy for tissue architecture mapping, hyper-plex fluorescence imaging for i...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-06-01
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| Series: | npj Imaging |
| Online Access: | https://doi.org/10.1038/s44303-025-00088-w |
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| author | Maomao Chen Hongqiang Ma Xuejiao Sun Marc Schwartz Randall E. Brand Jianquan Xu Dimitrios S. Gotsis Phuong Nguyen Beverley A. Moore Lori Snyder Rhonda M. Brand Yang Liu |
| author_facet | Maomao Chen Hongqiang Ma Xuejiao Sun Marc Schwartz Randall E. Brand Jianquan Xu Dimitrios S. Gotsis Phuong Nguyen Beverley A. Moore Lori Snyder Rhonda M. Brand Yang Liu |
| author_sort | Maomao Chen |
| collection | DOAJ |
| description | Abstract Multi-modal, multiscale imaging is crucial for quantitative high-content spatial profiling. We present an integrated image processing pipeline for comprehensive tissue analysis that combines quantitative phase microscopy for tissue architecture mapping, hyper-plex fluorescence imaging for immune microenvironment profiling, and whole-slide histopathology. This approach enables detailed morphological mapping of tissue architecture and cell morphology, while simultaneously linking them to the functional states of individual cells across the entire slide. By analyzing tissue biopsies from patients with ulcerative colitis, we demonstrate the potential of this pipeline for quantitative spatial analysis of molecular markers related to mucosal healing. Open-source and compatible with conventional microscopy systems, this pipeline provides a powerful tool for research and clinical applications through its comprehensive integration of quantitative, high-content, and histological imaging modalities. |
| format | Article |
| id | doaj-art-49a33b20e26b4dc28bc56d84b65a65ff |
| institution | DOAJ |
| issn | 2948-197X |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | npj Imaging |
| spelling | doaj-art-49a33b20e26b4dc28bc56d84b65a65ff2025-08-20T02:40:15ZengNature Portfolionpj Imaging2948-197X2025-06-013111610.1038/s44303-025-00088-wMultimodal whole slide image processing pipeline for quantitative mapping of tissue architecture and tissue microenvironmentMaomao Chen0Hongqiang Ma1Xuejiao Sun2Marc Schwartz3Randall E. Brand4Jianquan Xu5Dimitrios S. Gotsis6Phuong Nguyen7Beverley A. Moore8Lori Snyder9Rhonda M. Brand10Yang Liu11Departments of Medicine and Bioengineering, University of PittsburghDepartments of Medicine and Bioengineering, University of PittsburghDepartments of Medicine and Bioengineering, University of PittsburghDepartment of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, University of Pittsburgh Medical CenterDepartment of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, University of Pittsburgh Medical CenterDepartments of Medicine and Bioengineering, University of PittsburghGrainger College of Engineering, Department of Electrical and Computer Engineering, University of Illinois Urbana-ChampaignDepartments of Medicine and Bioengineering, University of PittsburghDepartment of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, University of Pittsburgh Medical CenterDepartment of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, University of Pittsburgh Medical CenterDepartment of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, University of Pittsburgh Medical CenterDepartments of Medicine and Bioengineering, University of PittsburghAbstract Multi-modal, multiscale imaging is crucial for quantitative high-content spatial profiling. We present an integrated image processing pipeline for comprehensive tissue analysis that combines quantitative phase microscopy for tissue architecture mapping, hyper-plex fluorescence imaging for immune microenvironment profiling, and whole-slide histopathology. This approach enables detailed morphological mapping of tissue architecture and cell morphology, while simultaneously linking them to the functional states of individual cells across the entire slide. By analyzing tissue biopsies from patients with ulcerative colitis, we demonstrate the potential of this pipeline for quantitative spatial analysis of molecular markers related to mucosal healing. Open-source and compatible with conventional microscopy systems, this pipeline provides a powerful tool for research and clinical applications through its comprehensive integration of quantitative, high-content, and histological imaging modalities.https://doi.org/10.1038/s44303-025-00088-w |
| spellingShingle | Maomao Chen Hongqiang Ma Xuejiao Sun Marc Schwartz Randall E. Brand Jianquan Xu Dimitrios S. Gotsis Phuong Nguyen Beverley A. Moore Lori Snyder Rhonda M. Brand Yang Liu Multimodal whole slide image processing pipeline for quantitative mapping of tissue architecture and tissue microenvironment npj Imaging |
| title | Multimodal whole slide image processing pipeline for quantitative mapping of tissue architecture and tissue microenvironment |
| title_full | Multimodal whole slide image processing pipeline for quantitative mapping of tissue architecture and tissue microenvironment |
| title_fullStr | Multimodal whole slide image processing pipeline for quantitative mapping of tissue architecture and tissue microenvironment |
| title_full_unstemmed | Multimodal whole slide image processing pipeline for quantitative mapping of tissue architecture and tissue microenvironment |
| title_short | Multimodal whole slide image processing pipeline for quantitative mapping of tissue architecture and tissue microenvironment |
| title_sort | multimodal whole slide image processing pipeline for quantitative mapping of tissue architecture and tissue microenvironment |
| url | https://doi.org/10.1038/s44303-025-00088-w |
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