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

DNA Microarrays02:34

DNA Microarrays

16.8K
Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
16.8K
Next-generation Sequencing03:00

Next-generation Sequencing

87.9K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
87.9K
X-ray Diffraction of Biological Samples01:10

X-ray Diffraction of Biological Samples

3.8K
X-ray diffraction or XRD is an analytical tool that utilizes X-rays to study ordered structures such as crystalline organic and inorganic samples, polycrystalline materials, proteins, carbohydrates, and drugs.
According to Bragg's law, when X-rays strike the sample positioned on a stage, the rays are  scattered by the electron clouds around the sample atoms. The  X-ray diffraction or scattering is caused by constructive interference of the X-ray waves that reflect off the internal...
3.8K
Imaging Biological Samples with Optical Microscopy01:18

Imaging Biological Samples with Optical Microscopy

9.1K
Optical microscopy uses optic principles to provide detailed images of samples. Antonie van Leeuwenhoek designed the first compound optical microscope in the 17th century to visualize blood cells, bacteria, and yeast cells. In 1830, Joseph Jackson Lister created an essentially modern light microscope. The 20th century saw the development of microscopes with enhanced magnification and resolution.
In optical microscopy, the specimen to be viewed is placed on a glass slide and clipped on the stage...
9.1K
Super-resolution Fluorescence Microscopy01:37

Super-resolution Fluorescence Microscopy

12.3K
Super-resolution fluorescence microscopy (SRFM) provides a better resolution than conventional fluorescence microscopy by reducing the point spread function (PSF). PSF is the light intensity distribution from a point that causes it to appear blurred. Due to PSF, each fluorescing point appears bigger than its actual size, and it is the PSF interference of nearby fluorophores that causes the blurred image. Various approaches to achieving higher resolution through SRFM have recently been...
12.3K
Three-Dimensional Microscopy in Microbiology01:28

Three-Dimensional Microscopy in Microbiology

907
Three-dimensional imaging techniques are essential in cell biology, allowing researchers to visualize intricate cellular structures with high resolution. Two prominent methods, Differential Interference Contrast Microscopy (DIC) and Confocal Scanning Laser Microscopy (CSLM), provide distinct advantages for imaging live and thick specimens, respectively.Differential Interference Contrast MicroscopyDIC microscopy enhances contrast in transparent, unstained samples by converting phase...
907

You might also read

Related Articles

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

Sort by
Same author

Bisphenol A induces a pro-angiogenic-like phenotype via the G protein-coupled receptor 30 (GPR30) pathway.

Scientific reports·2026
Same author

Exploration of miR-326 delivery via biocompatible polymeric nanoparticles in medulloblastoma: A preliminary study.

Molecular therapy. Nucleic acids·2026
Same author

Circulating EV-microRNAs are dynamic biomarkers of resistance to therapeutic immunomodulation in metastatic melanoma.

Communications medicine·2026
Same author

The history and function of a circular RNA.

Nature communications·2026
Same author

Modeling pediatric low-grade glioma heterogeneity using human forebrain organoids.

Molecular cancer·2026
Same author

A 3D morphogenetic blueprint for metastatic outgrowth in breast cancer.

Cell·2026
Same journal

Whole-cell particle-based digital twin simulations from 4D lattice light-sheet microscopy data.

Cell·2026
Same journal

Systematic discovery of pathogen effector functions across human pathogens and pathways.

Cell·2026
Same journal

Structural basis for host membrane binding and remodeling by invading malaria parasites.

Cell·2026
Same journal

Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning.

Cell·2026
Same journal

Arc mediates intercellular tau transmission via extracellular vesicles.

Cell·2026
Same journal

Electromagnetic field-inducible in vivo gene switch for remote spatiotemporal control of gene expression.

Cell·2026
See all related articles

Related Experiment Video

Updated: May 2, 2026

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
09:19

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Published on: July 6, 2022

4.9K

Open-ST: High-resolution spatial transcriptomics in 3D.

Marie Schott1, Daniel León-Periñán1, Elena Splendiani2

  • 1Laboratory for Systems Biology of Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association (MDC), Hannoversche Str. 28, 10115 Berlin, Germany.

Cell
|June 25, 2024
PubMed
Summary
This summary is machine-generated.

Open-ST provides an open-source spatial transcriptomics (ST) method for high-resolution, cost-efficient tissue analysis. This tool enables 3D reconstruction and reveals cellular organization in health and disease.

Keywords:
HNSCCcancermetastasisopen sourceresourcesingle cellspatial transcriptomicssubcellularthree dimensional

More Related Videos

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C
09:32

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

Published on: October 14, 2022

3.4K
Author Spotlight: Exploring Advanced Therapeutic Targets in Osteosarcoma Through Spatial Transcriptomics
07:43

Author Spotlight: Exploring Advanced Therapeutic Targets in Osteosarcoma Through Spatial Transcriptomics

Published on: May 3, 2024

2.7K

Related Experiment Videos

Last Updated: May 2, 2026

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
09:19

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Published on: July 6, 2022

4.9K
Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C
09:32

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

Published on: October 14, 2022

3.4K
Author Spotlight: Exploring Advanced Therapeutic Targets in Osteosarcoma Through Spatial Transcriptomics
07:43

Author Spotlight: Exploring Advanced Therapeutic Targets in Osteosarcoma Through Spatial Transcriptomics

Published on: May 3, 2024

2.7K

Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Spatial transcriptomics (ST) methods are crucial for understanding tissue complexity.
  • Existing ST methods face challenges in ease of use, resolution, cost, and 3D scalability.

Purpose of the Study:

  • To introduce Open-ST, an open-source, sequencing-based resource for 2D and 3D spatial transcriptomics.
  • To address the need for high-resolution, cost-efficient, and scalable ST methods.

Main Methods:

  • Development of an open-source experimental and computational framework called Open-ST.
  • Application of Open-ST to mouse brain for subcellular resolution transcript capture.
  • Utilized Open-ST on head-and-neck tumors and lymph nodes for immune, stromal, and tumor cell population analysis.

Main Results:

  • Open-ST achieved subcellular resolution in mouse brain, enabling cell type reconstruction.
  • Successfully captured diverse cell populations in tumors and lymph nodes, validated by imaging ST.
  • Identified spatial organization of cell states around communication hotspots in tumors.
  • 3D reconstruction of metastatic lymph nodes revealed structures and biomarkers at the tumor boundary not visible in 2D.

Conclusions:

  • Open-ST offers a versatile and accessible platform for advanced spatial transcriptomics research.
  • The method provides high-resolution insights into tissue organization and cellular interactions in both 2D and 3D.
  • Open-ST facilitates the discovery of novel biomarkers and understanding of disease mechanisms at a spatial level.