IBEX: an iterative immunolabeling and chemical bleaching method for high-content imaging of diverse tissues

Highly multiplexed tissue imaging using repeated oligonucleotide exchange reaction

(2021) Julia Kennedy‐Darling et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Highly Multiplexed Phenotyping of Immunoregulatory Proteins in the Tumor Microenvironment by CODEX Tissue Imaging

(2021) Darci Phillips et al.   Frontiers in Immunology

CODEX multiplexed tissue imaging with DNA-conjugated antibodies

(2021) Sarah Black et al.   Nature Protocols

Anatomical structures, cell types and biomarkers of the Human Reference Atlas

(2021) Katy Börner et al.   NATURE CELL BIOLOGY

Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging

(2021) John W. Hickey et al.   NATURE METHODS

The single-cell pathology landscape of breast cancer

(2020) Hartland W. Jackson et al.   NATURE

The Society for Immunotherapy in Cancer statement on best practices for multiplex immunohistochemistry (IHC) and immunofluorescence (IF) staining and validation

(2020) Janis M Taube et al.   Journal for ImmunoTherapy of Cancer

Overview of multiplex immunohistochemistry/immunofluorescence techniques in the era of cancer immunotherapy

(2020) Wei Chang Colin Tan et al.   Cancer Communications

Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front

(2020) Christian M. Schürch et al.   CELL

Commensal-driven immune zonation of the liver promotes host defence

(2020) Anita Gola et al.   NATURE

IBEX: A versatile multiplex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues

(2020) Andrea J. Radtke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resident Macrophages Cloak Tissue Microlesions to Prevent Neutrophil-Driven Inflammatory Damage

(2019) Stefan Uderhardt et al.   CELL

The Chemoattractant Receptor Ebi2 Drives Intranodal Naive CD4+ T Cell Peripheralization to Promote Effective Adaptive Immunity

(2019) Antonio P. Baptista et al.   IMMUNITY

Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues

(2019) Sinem K. Saka et al.   NATURE BIOTECHNOLOGY

Qualifying antibodies for image-based immune profiling and multiplexed tissue imaging

(2019) Ziming Du et al.   Nature Protocols

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

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Toward a Common Coordinate Framework for the Human Body

(2019) Jennifer E. Rood et al.   CELL

Robust blind spectral unmixing for fluorescence microscopy using unsupervised learning

(2019) Tristan D. McRae et al.   PLoS One

Spatial distribution and function of T follicular regulatory cells in human lymph nodes

(2018) Ismail Sayin et al.   JOURNAL OF EXPERIMENTAL MEDICINE

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

Innate and adaptive lymphocytes sequentially shape the gut microbiota and lipid metabolism

(2018) Kairui Mao et al.   NATURE

Multiplexed protein maps link subcellular organization to cellular states

(2018) Gabriele Gut et al.   SCIENCE

SimpleITK Image-Analysis Notebooks: a Collaborative Environment for Education and Reproducible Research

(2017) Ziv Yaniv et al.   JOURNAL OF DIGITAL IMAGING

Multiplex Staining by Sequential Immunostaining and Antibody Removal on Routine Tissue Sections

(2017) Maddalena Maria Bolognesi et al.   JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY

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

(2017) Denis Schapiro et al.   NATURE METHODS

Follicular CD8 T cells accumulate in HIV infection and can kill infected cells in vitro via bispecific antibodies

(2017) Constantinos Petrovas et al.   Science Translational Medicine

Quantitative Multiplex Immunohistochemistry Reveals Myeloid-Inflamed Tumor-Immune Complexity Associated with Poor Prognosis

(2017) Takahiro Tsujikawa et al.   Cell Reports

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Multiplexed Epitope-Based Tissue Imaging for Discovery and Healthcare Applications

(2016) Bernd Bodenmiller   Cell Systems

Simple, Scalable Proteomic Imaging for High-Dimensional Profiling of Intact Systems

(2015) Evan Murray et al.   CELL

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Lymph-Node Resident CD8α+ Dendritic Cells Capture Antigens from Migratory Malaria Sporozoites and Induce CD8+ T Cell Responses

(2015) Andrea J. Radtke et al.   PLoS Pathogens

Multiplexed ion beam imaging of human breast tumors

(2014) Michael Angelo et al.   NATURE MEDICINE

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

(2014) Charlotte Giesen et al.   NATURE METHODS

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

The Design of SimpleITK

(2013) Bradley C. Lowekamp et al.   Frontiers in Neuroinformatics

A Spatially-Organized Multicellular Innate Immune Response in Lymph Nodes Limits Systemic Pathogen Spread

(2012) Wolfgang Kastenmüller et al.   CELL

Histo-Cytometry: A Method for Highly Multiplex Quantitative Tissue Imaging Analysis Applied to Dendritic Cell Subset Microanatomy in Lymph Nodes

(2012) Michael Y. Gerner et al.   IMMUNITY

Ultrabright photoactivatable fluorophores created by reductive caging

(2012) Joshua C Vaughan et al.   NATURE METHODS

Blind Source Separation Techniques for the Decomposition of Multiply Labeled Fluorescence Images

(2009) Richard A. Neher et al.   BIOPHYSICAL JOURNAL

Efficient subpixel image registration algorithms

(2008) Manuel Guizar-Sicairos et al.   OPTICS LETTERS