Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Single-cell spatial pharmacobiology identifies conserved stromal barriers to therapeutic antibody delivery in human solid tumors.

Nature biotechnology·2026
Same author

Immune Checkpoint Therapy Drives Maturation of a Cellular Neighborhood Nucleated by T Cell-APC Triads Enabling Spatially Compartmentalized Tumor Immunity.

bioRxiv : the preprint server for biology·2026
Same author

High-dimensional spatiotemporal single-cell atlas and 3D imaging of the bone marrow microenvironment during CML progression.

Blood·2026
Same author

Multi-scaled transcriptomics of chronically inflamed nasal epithelium reveals immune-epithelial dynamics and tissue remodeling in nasal polyp formation.

Immunity·2025
Same author

Autoimmune origin for immune checkpoint inhibitor-diabetes revealed by deep immune phenotyping of the pancreas.

Journal for immunotherapy of cancer·2025
Same author

The commitment of the human cell atlas to humanity.

Nature communications·2024

Related Experiment Video

Updated: Aug 20, 2025

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
05:53

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

10.2K

Highly multiplexed spatial profiling with CODEX: bioinformatic analysis and application in human disease.

Wilson Kuswanto1,2, Garry Nolan2,3, Guolan Lu4,5,6

  • 1Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, 94304, USA.

Seminars in Immunopathology
|November 22, 2022
PubMed
Summary
This summary is machine-generated.

Multiplexed imaging with CODEX visualizes over 50 cellular markers for spatial analysis in tissues. This technology aids understanding of cancer, autoimmunity, and infection, with evolving bioinformatics approaches.

Keywords:
CODEXCell segmentationCellular neighborhoodsSpatial analysisSpatial profilingTissue immunology

More Related Videos

Multiplexed Barcoding Image Analysis for Immunoprofiling and Spatial Mapping Characterization in the Single-Cell Analysis of Paraffin Tissue Samples
08:18

Multiplexed Barcoding Image Analysis for Immunoprofiling and Spatial Mapping Characterization in the Single-Cell Analysis of Paraffin Tissue Samples

Published on: April 7, 2023

1.7K
Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq
06:24

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Published on: March 12, 2021

3.7K

Related Experiment Videos

Last Updated: Aug 20, 2025

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
05:53

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

10.2K
Multiplexed Barcoding Image Analysis for Immunoprofiling and Spatial Mapping Characterization in the Single-Cell Analysis of Paraffin Tissue Samples
08:18

Multiplexed Barcoding Image Analysis for Immunoprofiling and Spatial Mapping Characterization in the Single-Cell Analysis of Paraffin Tissue Samples

Published on: April 7, 2023

1.7K
Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq
06:24

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Published on: March 12, 2021

3.7K

Area of Science:

  • Biomedical imaging
  • Molecular biology
  • Bioinformatics

Background:

  • Multiplexed imaging provides spatial context for cellular and molecular data.
  • Existing multi-omic technologies are complemented by spatial profiling.
  • Understanding health and disease is deepened by single-cell spatial localization.

Purpose of the Study:

  • To review the applications of CODEX (CO-Detection by Indexing) technology.
  • To discuss bioinformatics approaches for analyzing multiplexed imaging data.
  • To highlight challenges and future directions in multiplexed spatial profiling.

Main Methods:

  • CODEX utilizes a microfluidics system with DNA barcoded antibodies.
  • Visualizes over 50 cellular markers at the single-cell level within tissues.
  • Covers data preprocessing, cell segmentation, marker quantification, and spatial analysis.

Main Results:

  • CODEX has been applied to studies in cancer, autoimmunity, and infection.
  • Various bioinformatics pipelines are available for multiplexed imaging data analysis.
  • Spatial analysis techniques reveal cellular interactions and tissue architecture.

Conclusions:

  • CODEX is a powerful tool for high-plex spatial biology.
  • Advancements in bioinformatics are crucial for interpreting complex spatial datasets.
  • Future developments will expand the capabilities of multiplexed spatial profiling.