3D tissue imaging literature
Publications shaping the future of tissue analysis.
A curated collection of scientific literature on 3D tissue imaging, digital pathology, spatial profiling, volumetric datasets, and quantitative tissue analysis.
Scientific literature
Publications advancing 3D tissue imaging and analysis
Explore peer-reviewed studies and relevant preprints covering whole-tissue imaging, 3D histology, spatial biology, digital pathology, multimodal profiling, and AI-powered quantitative analysis.
3D histology and whole-tissue imaging
Tissue processing, intact-sample imaging, volumetric pathology, microdissection, and evidence comparing 2D sampling with 3D tissue assessment.
- 2026 arXiv preprint
Extracting and analyzing 3D histomorphometric features related to perineural and lymphovascular invasion in prostate cancer
Chow, S. S. L., et al. arXiv:2603.06936, 2026.
View paper - 2026 bioRxiv preprint
Assessing the effects of a 3D pathology tissue-processing workflow on downstream molecular analyses
Baraznenok, E., et al. bioRxiv preprint, 2026.
View paper - 2025 bioRxiv preprint
3D pathology-guided microdissection
Hsieh, H.-C., et al. bioRxiv preprint, 2025.
View paper - 2024 Editorial
Tissue histology in 3D
Nature Methods 21, 1133, 2024.
View editorial - 2024 Review
Deep 3D histology powered by tissue clearing, omics and AI
Ertürk, A. Nature Methods 21, 1153–1165, 2024.
View paper - 2024 Research article
Beyond 2D: A scalable and highly sensitive method for a comprehensive 3D analysis of kidney biopsy tissue
Yamada, H., et al. PNAS Nexus 3, pgad433, 2024.
View paper - 2024 Research article
Efficient 3D imaging and pathological analysis of the human lymphoma tumor microenvironment using light-sheet immunofluorescence microscopy
Chen, L., et al. Theranostics 14, 406–419, 2024.
View paper - 2025 Research article
Three-dimensional assessments are necessary to determine the true, spatially resolved composition of tissues
Forjaz, A., et al. Cell Reports Methods 5, 101075, 2025.
View paper
Digital pathology and spatial biology
Multiplexed tissue profiling, spatial transcriptomics, multimodal imaging, tumor microenvironments, immune niches, and full-volume molecular mapping.
- 2025 Research article
Highly multiplexed 3D profiling of cell states and immune niches in human tumors
Yapp, C., Nirmal, A. J., Zhou, F., et al. Nature Methods 22, 2180–2193, 2025.
View paper - 2025 Research article
Combining spatial transcriptomics and ECM imaging in 3D for mapping cellular interactions in the tumor microenvironment
Pentimalli, T. M., et al. Cell Systems 16, 101261, 2025.
View paper - 2025 arXiv preprint
AI-driven 3D Spatial Transcriptomics
Almagro-Pérez, C., Song, A. H., Weishaupt, L., et al. arXiv:2502.17761, 2025.
View paper - 2024 Research article
INSIHGT: an accessible multi-scale, multi-modal 3D spatial biology platform
Yau, C. N., Hung, J. T. S., Campbell, R. A. A., et al. Nature Communications 15, 10888, 2024.
View paper - 2024 Research article
Tumour evolution and microenvironment interactions in 2D and 3D space
Mo, C.-K., et al. Nature 634, 1178–1186, 2024.
View paper - 2024 Research article
Molecular, metabolic, and subcellular mapping of the tumor immune microenvironment via 3D targeted and non-targeted multiplex multi-omics analyses
Ferri-Borgogno, S., et al. Cancers 16, 846, 2024.
View paper - 2023 Research article
Multiplexed 3D atlas of state transitions and immune interaction in colorectal cancer
Lin, J. R., et al. Cell 186, 363–381.e19, 2023.
View paper - 2023 bioRxiv preprint
High-resolution molecular atlas of a lung tumor in 3D
Pentimalli, T. M., et al. bioRxiv preprint, 2023.
View paper
AI-powered analysis and quantitative outputs
Deep learning, triage, annotation, cell mapping, quantitative PD-L1 analysis, and computational interpretation of large volumetric pathology datasets.
- 2025 Preprint
Deep-learning triage of 3D pathology datasets for comprehensive and efficient pathologist assessments
Gao, G., et al. bioRxiv preprint, 2025.
View paper - 2024 Research article
Virtual reality-empowered deep-learning analysis of brain cells
Kaltenecker, D., et al. Nature Methods 21, 1306–1315, 2024.
View paper - 2024 Research briefing
Simplifying deep learning to enhance accessibility of large-scale 3D brain imaging analysis
Nature Methods 21, 1151–1152, 2024.
View paper - 2024 Comment
Realization of cellomics to dive into the whole-body or whole-organ cell cloud
Mitani, T. T., Susaki, E. A., Matsumoto, K., et al. Nature Methods 21, 1138–1142, 2024.
View paper - 2024 Research article
Analysis of 3D pathology samples using weakly supervised AI
Song, A. H., et al. Cell 187, 2502–2520.e17, 2024.
View paper - 2024 Research article
A novel computer-assisted tool for 3D imaging of programmed death-ligand 1 expression in immunofluorescence-stained and optically cleared breast cancer specimens
Lee, Y. H., et al. BMC Cancer 24, 121, 2024.
View paper - 2024 Perspective
The 3D Revolution in Cancer Discovery
Wang, L., et al. Cancer Discovery 14, 625–629, 2024.
View paper - 2022 Research article
Computer-assisted three-dimensional quantitation of programmed death-ligand 1 in non-small cell lung cancer using tissue clearing technology
Lin, Y. Y., et al. Journal of Translational Medicine 20, 131, 2022.
View paper
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