Squidpy: a scalable framework for spatial omics analysis

Spatially resolved single-cell genomics and transcriptomics by imaging

(2021) Xiaowei Zhuang   NATURE METHODS

Spatially resolved transcriptomics adds a new dimension to genomics

(2021) Ludvig Larsson et al.   NATURE METHODS

sepal: Identifying Transcript Profiles with Spatial Patterns by Diffusion-based Modeling

(2021) Alma Anderson et al.   BIOINFORMATICS

Spatial Transcriptomics: Molecular Maps of the Mammalian Brain

(2021) Cantin Ortiz et al.   Annual Review of Neuroscience

Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis

(2021) Dénes Türei et al.   Molecular Systems Biology

Spatial transcriptomics at subspot resolution with BayesSpace

(2021) Edward Zhao et al.   NATURE BIOTECHNOLOGY

Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis

(2021) T. Lohoff et al.   NATURE BIOTECHNOLOGY

Cell segmentation-free inference of cell types from in situ transcriptomics data

(2021) Jeongbin Park et al.   Nature Communications

Cell segmentation in imaging-based spatial transcriptomics

(2021) Viktor Petukhov et al.   NATURE BIOTECHNOLOGY

Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram

(2021) Tommaso Biancalani et al.   NATURE METHODS

The single-cell pathology landscape of breast cancer

(2020) Hartland W. Jackson et al.   NATURE

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

(2020) Mirjana Efremova et al.   Nature Protocols

TissUUmaps: Interactive visualization of large-scale spatial gene expression and tissue morphology data

(2020) Leslie Solorzano et al.   BIOINFORMATICS

Seamless integration of image and molecular analysis for spatial transcriptomics workflows

(2020) Joseph Bergenstråhle et al.   BMC GENOMICS

Array programming with NumPy

(2020) Charles R. Harris et al.   NATURE

Single-cell metabolic profiling of human cytotoxic T cells

(2020) Felix J. Hartmann et al.   NATURE BIOTECHNOLOGY

High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue

(2020) Yang Liu et al.   CELL

Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2

(2020) Robert R. Stickels et al.   NATURE BIOTECHNOLOGY

Cellpose: a generalist algorithm for cellular segmentation

(2020) Carsen Stringer et al.   NATURE METHODS

Single-Nucleus and In Situ RNA–Sequencing Reveal Cell Topographies in the Human Pancreas

(2020) Luca Tosti et al.   GASTROENTEROLOGY

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

MIBI-TOF: A multiplexed imaging platform relates cellular phenotypes and tissue structure

(2019) Leeat Keren et al.   Science Advances

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

CellProfiler 3.0: Next-generation image processing for biology

(2018) Claire McQuin et al.   PLOS BIOLOGY

Multiplexed protein maps link subcellular organization to cellular states

(2018) Gabriele Gut et al.   SCIENCE

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

(2018) Jeffrey R. Moffitt et al.   SCIENCE

histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data

(2017) Denis Schapiro et al.   NATURE METHODS

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Mass Cytometry: Single Cells, Many Features

(2016) Matthew H. Spitzer et al.   CELL

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry

(2014) Charlotte Giesen et al.   NATURE METHODS

scikit-image: image processing in Python

(2014) Stéfan van der Walt et al.   PeerJ