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Related Concept Videos

Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Electron Microscope Tomography and Single-particle Reconstruction01:07

Electron Microscope Tomography and Single-particle Reconstruction

Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
Electron Tomography
Electron tomography can be performed either in TEM or STEM (scanning transmission...
X-ray Diffraction of Biological Samples01:10

X-ray Diffraction of Biological Samples

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 crystal...
Two-Dimensional Microscopy in Microbiology01:29

Two-Dimensional Microscopy in Microbiology

Two-dimensional (2D) microscopy encompasses a range of optical techniques that capture images within a single focal plane, offering detailed representations of microscopic structures. These techniques are essential in biological and medical research, enabling the visualization of cellular and subcellular structures with different levels of contrast and specificity.There are several major types of 2D microscopy, each with strengths and applications.Bright-Field MicroscopyBright-field microscopy...

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Related Experiment Video

Updated: Jul 13, 2026

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

Published on: July 6, 2022

Odon: An ultra-fast viewer for spatial proteomics.

Alexander Coulton1, Nicholas McGranahan1

  • 1UCL Cancer Institute, Paul O'Gorman Building, 72 Huntley St, London WC1E 6DD.

Bioinformatics (Oxford, England)
|July 11, 2026
PubMed
Summary

Odon is a new desktop viewer for exploring large spatial proteomics and transcriptomics imaging datasets on a standard laptop. It offers efficient visualization and analysis, outperforming existing tools in memory usage and loading speed.

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Non-invasive 3D-Visualization with Sub-micron Resolution Using Synchrotron-X-ray-tomography

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Related Experiment Videos

Last Updated: Jul 13, 2026

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

Published on: July 6, 2022

Mining Spatial Transcriptomics Datasets using DeepSpaceDB
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Mining Spatial Transcriptomics Datasets using DeepSpaceDB

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Non-invasive 3D-Visualization with Sub-micron Resolution Using Synchrotron-X-ray-tomography
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Non-invasive 3D-Visualization with Sub-micron Resolution Using Synchrotron-X-ray-tomography

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Area of Science:

  • Computational biology
  • Bioinformatics
  • Data visualization

Background:

  • Multiplexed spatial imaging generates large, high-dimensional datasets.
  • Efficient visualization is crucial for identifying staining artifacts and analyzing data at scale.

Purpose of the Study:

  • To develop a high-performance desktop viewer for rapid, interactive exploration of multiplex imaging data.
  • To enable efficient analysis of spatial proteomics and transcriptomics datasets on standard hardware.

Main Methods:

  • Developed Odon, a native Rust desktop viewer utilizing the OME-Zarr format.
  • Implemented viewport-driven tile loading and GPU-based compositing for optimized rendering.
  • Supported GeoJSON, GeoParquet, SpatialData, Xenium containers, and TIFF formats.

Main Results:

  • Odon demonstrated lower peak memory use and faster warm-start image loading compared to napari and QuPath.
  • Achieved smooth rendering and interaction with over 1,000,000 segmented cells.
  • Integrated visual analytics features like live thresholding and mosaic mode for cohort studies.

Conclusions:

  • Odon provides a scalable, high-performance platform for visualizing and analyzing large multiplex imaging datasets.
  • Its efficient design facilitates rapid exploration and artifact detection on standard laptops.
  • Enables advanced visual analytics for cohort and tissue microarray studies.