Identifying 3D signal overlaps in spatial transcriptomics data with ovrlpy

Vandereyken, K., Sifrim, A., Thienpont, B. & Voet, T. Methods and applications for single-cell and spatial multi-omics. Nat. Reverend Genet. 24494-515 (2023).

Article CAS PubMed Google Scholar

Chen, H., Li, D. & Bar-Joseph, Z. SCS: cell segmentation for high-resolution spatial transcriptomics. Nat. Methods 201237-1243 (2023).

Article CAS PubMed Google Scholar

Fang, S. et al. Computational approaches and challenges in spatial transcriptomics. Genome. Proteome. Bioinform. 2124-47 (2023).

Google Scholar article

Fu, X. et al. BIDCell: Biologically informed self-supervised learning for segmentation of subcellular spatial transcriptomics data. Nat. Common. 15509 (2024).

Article CAS PubMed PubMed Central Google Scholar

Shu, J., Fu, H., Qiu, G., Kaye, P. and Ilyas, M. Segmentation of overlapping cell nuclei in digital histopathological images. Ann. Int. Conf. IEEE Eng. Med. Biol. Soc. 20135445-5448 (2013).

PubMed Google Scholar

Palokangas, S., Selinummi, J. & Yli-Harja, O. Fold segmentation in tissue section images. Ann. Int. Conf. IEEE Eng. Med. Biol. Soc. 20075642-5645 (2007).

PubMed Google Scholar

Taqi, SA, Sami, SA, Sami, LB & Zaki, SA A review of artifacts in histopathology. J. Oral maxillofac. Pathol. 22279 (2018).

Article PubMed PubMed Central Google Scholar

Moses, L. & Pachter, L. Museum of Spatial Transcriptomics. Nat. Methods 19534-546 (2022).

Article CAS PubMed Google Scholar

Yao, Z. et al. A high-resolution transcriptomic and spatial atlas of cell types throughout the mouse brain. Nature 624317-332 (2023).

Article CAS PubMed PubMed Central Google Scholar

Allen, NJ & Lyons, DA Glia as architects of central nervous system formation and function. Science 362181-185 (2018).

Article CAS PubMed PubMed Central Google Scholar

Megı́as, M., Emri, Z., Freund, TF & Gulyás, AI Total number and distribution of inhibitory and excitatory synapses on hippocampal CA1 pyramidal cells. Neuroscience 102527-540 (2001).

Article PubMed Google Scholar

Park, J. et al. Cell type inference without cell segmentation from in situ transcriptomic data. Nat. Common. 123545 (2021).

Article CAS PubMed PubMed Central Google Scholar

Müller-Bötticher, N., Tiesmeyer, S., Eils, R. & Ishaque, N. Sainsc: a computational tool for segmentation-free analysis of in situ capture data. Small methods 92401123 (2025).

Article PubMed Google Scholar

Petukhov, V. et al. Cell segmentation in imaging-based spatial transcriptomics. Nat. Biotechnology. 40345-354 (2022).

Article CAS PubMed Google Scholar

Jones, DC et al. Cell simulation as cell segmentation. Nat. Methods 221331-1342 (2025).

Article CAS PubMed PubMed Central Google Scholar

Wolock, SL, Lopez, R. & Klein, A.M. Scrublet: computational identification of cellular doublets in single-cell transcriptomic data. Cellular system. 8281-291 (2019).

Article CAS PubMed PubMed Central Google Scholar

Marco Salas, S. et al. Optimizing the Xenium In-Place Data Utility with best practice quality assessment and analysis workflows. Nat. Methods 22813-823 (2025).

Article CAS PubMed PubMed Central Google Scholar

Mitchel, J., Gao, T., Petukhov, V., Cole, E. & Kharchenko, PV Impact and correction of segmentation errors in spatial transcriptomics. Nat. Broom. https://doi.org/10.1038/s41588-025-02497-4 (2026).

Fresh frozen mouse brain replicas, in situ gene expression dataset analyzed using Xenium Onboard Analysis 1.0.2 (10x Genomics, 2023).

Pokrajac, NT, Tokarew, NJA, Gurdita, A., Ortin-Martinez, A. & Wallace, VA Meningeal macrophages inhibit chemokine signaling in pretumoral cells to suppress mouse medulloblastoma initiation. Dev. Cell 582015-2031 (2023).

Article CAS PubMed Google Scholar

Remsik, J. et al. Characterization, isolation and in vitro culture of leptomeningeal fibroblasts. J. Neuroimmunol. 361577727 (2021).

Article CAS PubMed PubMed Central Google Scholar

Tiklová, K. et al. Single-cell transcriptomics identifies stem cell-derived graft composition in a model of Parkinson’s disease. Nat. Common. 112434 (2020).

Article PubMed PubMed Central Google Scholar

Pietilä, R. et al. Molecular anatomy of adult mouse leptomeninges. Neuron 1113745-3764.e7 (2023).

Article PubMed Google Scholar

Howe, JR et al. Control of innate olfactory valence by separate cortical amygdalar circuits. Preprint at bioRxiv https://doi.org/10.1101/2024.06.26.600895 (2024).

Mah, CK et al. Bento: a toolbox for subcellular analysis of spatial transcriptomics data. Genome Biol. 2582 (2024).

Article CAS PubMed PubMed Central Google Scholar

Vizgen Data Version V1.0 (Vizgen, 2021).

Vizgen post-processing tool (Vizgen, 2025).

Whole mouse puppy (FFPE) with 5 K Mouse Pan Tissue and Pathway Panel and Snap25a/Snap25b Add-on, In Situ Gene Expression Dataset Analyzed Using Xenium Onboard Analysis 3.0.0 (10x Genomics, 2024).

Moffitt, JR et al. Molecular, spatial and functional single-cell profiling of the hypothalamic preoptic region. Science 362eaau5324 (2018).

Article PubMed PubMed Central Google Scholar

Moffitt, JR et al. Data from: single-cell molecular, spatial and functional profiling of the hypothalamic preoptic region. Dryad https://doi.org/10.5061/dryad.8t8s248 (2018).

Park, J. et al. Additional data for: segmentation-free inference of cell types from in situ transcriptomic data. Zenodo https://doi.org/10.5281/zenodo.3478502 (2019).

Tiesmeyer, S. & Müller-Bötticher, N. Data to recreate “2D, or not 2D?” Investigation of vertical signal integrity of tissue slices. Zenodo https://doi.org/10.5281/zenodo.16736589 (2025).