BANKSY unifies cell typing and tissue domain segmentation for scalable spatial omics data analysis

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Human organoids: model systems for human biology and medicine

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Robust decomposition of cell type mixtures in spatial transcriptomics

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Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis

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Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region

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Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system

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Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex

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SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network

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Individual brain organoids reproducibly form cell diversity of the human cerebral cortex

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A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

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Organoids

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Spatial transcriptomics at subspot resolution with BayesSpace

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Orchestrating single-cell analysis with Bioconductor

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Giotto: a toolbox for integrative analysis and visualization of spatial expression data

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Spatially organized multicellular immune hubs in human colorectal cancer

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The Matthews correlation coefficient (MCC) is more reliable than balanced accuracy, bookmaker informedness, and markedness in two-class confusion matrix evaluation

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dbscan: Fast Density-Based Clustering with R

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High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging

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Deciphering spatial domains from spatially resolved transcriptomics with an adaptive graph attention auto-encoder

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Robust mapping of spatiotemporal trajectories and cell–cell interactions in healthy and diseased tissues

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Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphST

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Cells of the human intestinal tract mapped across space and time

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Macrophage and neutrophil heterogeneity at single-cell spatial resolution in human inflammatory bowel disease

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Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease

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Organization of the human intestine at single-cell resolution

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Giotto, a toolbox for integrative analysis and visualization of spatial expression dataPreprint

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scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured

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SpiceMix enables integrative single-cell spatial modeling of cell identity

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A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex

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Clustering spatial transcriptomics data

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Torch.manual_seed(3407) is all you need: On the influence of random seeds in deep learning architectures for computer visionPreprint

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The Roles of Lpar1 in Central Nervous System Disorders and Diseases

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A Review of Convolutional Neural Networks and Gabor Filters in Object Recognition

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Macrophage Subpopulation Dynamics Shift following Intravenous Infusion of Mesenchymal Stromal Cells

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N‐myc downstream regulated family member 1 (<scp>NDRG1</scp>) is enriched in myelinating oligodendrocytes and impacts myelin degradation in response to demyelination

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Clustering the cortical laminae: in vivo parcellation

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Processed single cell data from CODEX multiplexed imaging of the human intestine

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Raw data and analysis scripts for the BANKSY spatial clustering package

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Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics

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Spatial transcriptomics reveals niche-specific enrichment and vulnerabilities of radial glial stem-like cells in malignant gliomas

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Computational approaches and challenges in spatial transcriptomics

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Spatial omics at the forefront: emerging technologies, analytical innovations, and clinical applications

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Benchmarking clustering, alignment, and integration methods for spatial transcriptomics

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Single-cell spatial transcriptomic profiling defines a pathogenic inflammatory niche in chronic active multiple sclerosis lesions

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Spatial architecture of development and disease

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Neurodevelopmental hijacking of oligodendrocyte lineage programs drives glioblastoma infiltration

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Non-invasive profiling of the tumour microenvironment with spatial ecotypes

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Graph attention automatic encoder based on contrastive learning for domain recognition of spatial transcriptomics

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Targeting Treg–fibroblast interaction to enhance immunotherapy in steatotic liver disease-related hepatocellular carcinoma

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High-Parameter Spatial Multi-Omics through Histology-Anchored Integration

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MNMST: topology of cell networks leverages identification of spatial domains from spatial transcriptomics data

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Quantitative characterization of tissue states using multiomics and ecological spatial analysis

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Protein-based classification reveals an immune-hot subtype in IDH mutant astrocytoma with worse prognosis

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Tissue module discovery in single-cell-resolution spatial transcriptomics data via cell-cell interaction-aware cell embedding

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Spatial biology – unravelling complexity within the glioblastoma microenvironment

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A comprehensive survey of dimensionality reduction and clustering methods for single-cell and spatial transcriptomics data

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SpatialLeiden: spatially aware Leiden clustering

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Cancer therapy resistance from a spatial‐omics perspective

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Spatial perturb-seq: single-cell functional genomics within intact tissue architecture

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SIMVI disentangles intrinsic and spatial-induced cellular states in spatial omics data

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stClinic dissects clinically relevant niches by integrating spatial multi-slice multi-omics data in dynamic graphs

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Systematic benchmarking of computational methods to identify spatially variable genes

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Targeting fibroblast derived thrombospondin 2 disrupts an immune-exclusionary environment at the tumor front in colorectal cancer

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Integrating histopathology and transcriptomics for spatial tumor microenvironment profiling in a melanoma case study

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Comparing Xenium 5K and Visium HD data from identical tissue slide at a pathological perspective

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StaVia: spatially and temporally aware cartography with higher-order random walks for cell atlases

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Cellular neighborhoods in cancer

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Learning tissue representation by identification of persistent local patterns in spatial omics data

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CellLENS enables cross-domain information fusion for enhanced cell population delineation in single-cell spatial omics data

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Bridging the dimensional gap from planar spatial transcriptomics to 3D cell atlases

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PCA-based spatial domain identification with state-of-the-art performance

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Bridging single cells to organs: Mesoscale modules as fundamental units of tissue function

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Points2Regions : Fast, interactive clustering of imaging‐based spatial transcriptomics data

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StereoSiTE: a framework to spatially and quantitatively profile the cellular neighborhood organized iTME

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Padlock Probe–Based Targeted In Situ Sequencing: Overview of Methods and Applications

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Cellular and Spatial Drivers of Unresolved Injury and Functional Decline in the Human KidneyPreprint

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Cellular senescence in human liver under normal aging and cancer

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Challenges and Opportunities in Analyzing Cancer-Associated Microbiomes

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ST-SCSR: identifying spatial domains in spatial transcriptomics data via structure correlation and self-representation

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Spatial transcriptomics reveals macrophage domestication by epithelial cells promotes immunotherapy resistance in small cell lung cancer

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Deciphering Spatial Domains by Integrating Histopathological Image and Transcriptomics via Contrastive LearningPreprint

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hoodscanR: profiling single-cell neighborhoods in spatial transcriptomics data

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Shared and unique transcriptomic signatures of antidepressant and probiotics action in the mammalian brain

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Spatially resolved molecular sex differences at single-cell resolution in the adult human ventromedial and arcuate hypothalamus

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Next‐generation spatial transcriptomics: unleashing the power to gear up translational oncology

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ONTraC characterizes spatially continuous variations of tissue microenvironment through niche trajectory analysis

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Spatially informed phenotyping by cyclic-in-situ-hybridisation identifies novel fibroblast populations and their pathogenic niches in systemic sclerosis

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Inferring spatial single-cell-level interactions through interpreting cell state and niche correlations learned by self-supervised graph transformer

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Towards a universal spatial molecular atlas of the mouse brainPreprint

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Cellular neighborhood analysis in spatial omics reveals new tissue domains and cell subtypes

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Reusability report: Exploring the transferability of self-supervised learning models from single-cell to spatial transcriptomics

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A comprehensive benchmarking for spatially resolved transcriptomics clustering methods across variable technologies, organs, and replicates

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Multi-omics-guided characterization of neoantigens improves patient stratification and potentiates combinatorial immunotherapy in glioma

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Spatial transcriptomics: integrating platforms and computational approaches for clinical insights

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Mapping biology in space: from spatial transcriptomics platforms to analytical tools and databases

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Spatial resolved transcriptomics: Computational insights into gene transcription across tissue and organ architecture in diverse applications

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High-parametric protein maps reveal the spatial organization in early-developing human lung

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Characterization of spatial homogeneous regions in tissues with concordex

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Single-cell spatial (scs) omics: Recent developments in data analysis

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Crosstalk of glutamine metabolism between cancer-associated fibroblasts and cancer cells

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GASTON-Mix: a unified model of spatial gradients and domains using spatial mixture-of-experts

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DECIPHER for learning disentangled cellular embeddings in large-scale heterogeneous spatial omics data

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Harnessing the potential of spatial statistics for spatial omics data with pasta

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Benchmarking multi-slice integration and downstream applications in spatial transcriptomics data analysis

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The interpretable multimodal dimension reduction framework SpaHDmap enhances resolution in spatial transcriptomics

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BANKSY: scalable cell typing and domain segmentation for spatial omics

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Clustering the cortical laminae: in vivo parcellation

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CellsFromSpace: a fast, accurate, and reference-free tool to deconvolve and annotate spatially distributed omics data

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A Deep Learning-based Pipeline for Segmenting the Cerebral Cortex Laminar Structure in Histology Images

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TrimNN: characterizing cellular community motifs for studying multicellular topological organization in complex tissues

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Charting the cardiac landscape: Advances in spatial transcriptomics for heart biology

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