3D Tissue Imaging Literature
The Latest Published Studies
Whether you're advancing clinical diagnostics, driving discovery in life sciences, or developing innovative tools, 3D tissue imaging is transforming how we see biology. This literature hub highlights cutting-edge research in 3D spatial biology, 3D histology, and digital pathology, showcasing how 3D spatial profiling unlocks insights that traditional 2D methods miss.
Here's what we're reading; let us know what's on your radar!
Huai-Ching Hsieh, et al. “3D pathology-guided microdissection” bioRxiv [Preprint]. 2025 Link.
Gao G, et al. "Deep-learning triage of 3D pathology datasets for comprehensive and efficient pathologist assessments.” bioRxiv [Preprint]. 2025 Link
Yapp, C., Nirmal, A.J., Zhou, F. et al. “Highly multiplexed 3D profiling of cell states and immune niches in human tumors." Nat Methods 22, 2180–2193 (2025). https://doi.org/10.1038/s41592-025-02824-x
Pentimalli, Tancredi Massimo et al. “Combining spatial transcriptomics and ECM imaging in 3D for mapping cellular interactions in the tumor microenvironment.” Cell systems, 101261. 9 Apr. 2025, doi:10.1016/j.cels.2025.101261. Link.
Cristina Almagro-Pérez, Andrew H. Song, Luca Weishaupt, Ahrong Kim, Guillaume Jaume, Drew F.K. Williamson, Konstantin Hemker, Ming Y. Lu, Kritika Singh, Bowen Chen, Long Phi Le, Alexander S. Baras, Sizun Jiang, Ali Bashashati, Jonathan T.C. Liu, Faisal Mahmood “AI-driven 3D Spatial Transcriptomics" https://doi.org/10.48550/arXiv.2502.17761 arXiv:2502.17761
Yau, C.N., Hung, J.T.S., Campbell, R.A.A. et al. “INSIHGT: an accessible multi-scale, multi-modal 3D spatial biology platform”. Nat Commun 15, 10888 (2024). https://doi.org/10.1038/s41467-024-55248-0. Link.
Chia-Kuei Mo, et al. “Tumour evolution and microenvironment interactions in 2D and 3D space”. Nature 634, 1178–1186 (2024). https://doi.org/10.1038/s41586-024-08087-4. Link
Nature Method Editorial: “Tissue Histology in 3D” Nature Methods volume 21, page1133 (2024)
Ertürk, A. Nat. Methods https://doi.org/10.1038/s41592-024-02327-1 (2024).
Kaltenecker, D. et al. Nat. Methods https://doi.org/10.1038/s41592-024-02245-2 (2024).
Nat. Methods https://doi.org/10.1038/s41592-024-02246-1 (2024).
Mitani, T. T., Susaki, E. A., Matsumoto, K. & Ueda, H. R. Nat. Methods https://doi.org/10.1038/s41592-024-02307-5 (2024).
Andrew H. Song et al. “Analysis of 3D pathology samples using weakly supervised AI”. Cell, Volume 187, Issue 10, 9 May 2024. Link
Ferri-Borgogno S. et al. “Molecular, Metabolic, and Subcellular Mapping of the Tumor Immune Microenvironment via 3D Targeted and Non-Targeted Multiplex Multi-Omics Analyses”. Cancers (Basel). 2024 Feb 20;16(5):846. doi: 10.3390/cancers16050846. PMID: 38473208; PMCID: PMC10930466. Link
Yamada H. et al. “Beyond 2D: A scalable and highly sensitive method for a comprehensive 3D analysis of kidney biopsy tissue”. PNAS Nexus. 2024 Jan 8;3(1):pgad433. doi: 10.1093/pnasnexus/pgad433. PMID: 38193136; PMCID: PMC10772983. Link
Chen L. et al. “Efficient 3D imaging and pathological analysis of the human lymphoma tumor microenvironment using light-sheet immunofluorescence microscopy.” Theranostics. 2024 Jan 1;14(1):406-419. doi: 10.7150/thno.86221. PMID: 38164148; PMCID: PMC10750216. Link
Lee, YH. et al. “A novel computer-assisted tool for 3D imaging of programmed death-ligand 1 expression in immunofluorescence-stained and optically cleared breast cancer specimens”. BMC Cancer 24, 121 (2024). https://doi.org/10.1186/s12885-023-11748-8 Link
Wang et al. "The 3D Revolution in Cancer Discovery." Cancer Discovery 14.4 (2024): 625-629. Link
André Forjaz et al. “Three-dimensional assessments are necessary to determine the true, spatially-resolved composition of tissues”. doi: https://doi.org/10.1101/2023.12.04.569986 Link
Lin JR et al. “Multiplexed 3D atlas of state transitions and immune interaction in colorectal cancer”. Cell. 2023 Jan 19;186(2):363-381.e19. doi: 10.1016/j.cell.2022.12.028. PMID: 36669472; PMCID: PMC10019067. Link
Tancredi Massimo Pentimalli et al. “High-resolution molecular atlas of a lung tumor in 3D”. (2023) doi: https://doi.org/10.1101/2023.05.10.539644 Link
Lin YY et al. “Computer-assisted three-dimensional quantitation of programmed death-ligand 1 in non-small cell lung cancer using tissue clearing technology”. J Transl Med. 2022 Mar 16;20(1):131. doi: 10.1186/s12967-022-03335-5. PMID: 35296339; PMCID: PMC8925228. Link
