Joint cell segmentation and cell type annotation for spatial transcriptomics

A community-based transcriptomics classification and nomenclature of neocortical cell types

(2020) Rafael Yuste et al.   NATURE NEUROSCIENCE

SpaGE: Spatial Gene Enhancement using scRNA-seq

(2020) Tamim Abdelaal et al.   NUCLEIC ACIDS RESEARCH

Zonation of Pancreatic Acinar Cells in Diabetic Mice

(2020) Adi Egozi et al.   Cell Reports

Spatial proteomics: a powerful discovery tool for cell biology

(2019) Emma Lundberg et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

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

Spatial transcriptomics coming of age

(2019) Darren J. Burgess   NATURE REVIEWS GENETICS

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

(2019) Joshua D. Welch et al.   CELL

Methods for Segmentation and Classification of Digital Microscopy Tissue Images

(2019) Quoc Dang Vu et al.   Frontiers in Bioengineering and Biotechnology

Split and merge watershed: A two-step method for cell segmentation in fluorescence microscopy images

(2019) Margarita Gamarra et al.   Biomedical Signal Processing and Control

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program

(2019)   NATURE

Probabilistic cell typing enables fine mapping of closely related cell types in situ

(2019) Xiaoyan Qian et al.   NATURE METHODS

A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart

(2019) Michaela Asp et al.   CELL

Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes

(2018) Jia-Ren Lin et al.   eLife

Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging

(2018) Yury Goltsev et al.   CELL

A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging

(2018) Leeat Keren et al.   CELL

Spatial Reconstruction of Single Enterocytes Uncovers Broad Zonation along the Intestinal Villus Axis

(2018) Andreas E. Moor et al.   CELL

Spatial organization of the somatosensory cortex revealed by osmFISH

(2018) Simone Codeluppi et al.   NATURE METHODS

Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections

(2018) Fredrik Salmén et al.   Nature Protocols

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

(2018) Jeffrey R. Moffitt et al.   SCIENCE

Perspectives on defining cell types in the brain

(2018) Eran A Mukamel et al.   CURRENT OPINION IN NEUROBIOLOGY

Single-cell spatial reconstruction reveals global division of labour in the mammalian liver

(2017) Keren Bahar Halpern et al.   NATURE

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

(2016) P. L. Stahl et al.   SCIENCE

Quantitative approaches for investigating the spatial context of gene expression

(2016) Je H. Lee   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

Integral split-and-merge methodology for real-time image segmentation

(2015) Fernando E. Correa-Tome et al.   JOURNAL OF ELECTRONIC IMAGING

Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues

(2015) Je Hyuk Lee et al.   Nature Protocols

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method

(2015) Jia-Ren Lin et al.   Nature Communications

Split-and-merge Procedure for Image Segmentation using Bimodality Detection Approach

(2014) D. Chaudhuri et al.   DEFENCE SCIENCE JOURNAL

Single-cell in situ RNA profiling by sequential hybridization

(2014) Eric Lubeck et al.   NATURE METHODS

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue

(2013) M. J. Gerdes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improved Automatic Detection and Segmentation of Cell Nuclei in Histopathology Images

(2009) Y. Al-Kofahi et al.   IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING