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Electron Microscope Tomography and Single-particle Reconstruction01:07

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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.
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Overview of Electron Microscopy01:25

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The wavelengths of visible light ultimately limit the maximum theoretical resolution of images created by light microscopes. Most light microscopes can only magnify 1000X, and a few can magnify up to 1500X. Electrons, like electromagnetic radiation, can behave like waves, but with wavelengths of 0.005 nm, they produce significantly greater resolution up to 0.05 nm as compared to 500 nm for visible light. An electron microscope (EM) can create a sharp image that is magnified up to 2,000,000X.
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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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Cryo-electron Microscopy01:28

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Conventional electron microscopy (EM) involves dehydration, fixation, and staining of biological samples, which distorts the native state of biological molecules and results in several artifacts. Also, the high-energy electron beam damages the sample and makes it difficult to obtain high-resolution images. These issues can be addressed using cryo-EM, which uses frozen samples and gentler electron beams. The technique was developed by Jacques Dubochet, Joachim Frank, and Richard Henderson, for...
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Updated: Mar 24, 2026

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Chart builder: an interactive tool for user driven data visualization in the electron microscopy data bank.

Neli Fonseca1, Amudha Kumari Duraisamy1, Zhe Wang1

  • 1Electron Microscopy Data Bank (EMDB), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridgeshire, United Kingdom.

Frontiers in Bioinformatics
|March 23, 2026
PubMed
Summary
This summary is machine-generated.

Chart Builder is a new web platform for visualizing 3D Electron Microscopy (3DEM) data. It allows researchers to explore and analyze metadata from EMDB and EMPIAR archives, creating publication-quality charts without coding.

Keywords:
FAIR (findable accessible interoperable andreusable) principlescryoEM (cryo-electron microscopy)data repositorydata visualizationgraph

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Area of Science:

  • Structural Biology
  • Biophysics
  • Data Science

Background:

  • The fields of cryogenic sample-electron microscopy (cryoEM) and 3D Electron Microscopy (3DEM) generate vast amounts of data archived in EMDB and EMPIAR.
  • Effective data exploration, analysis, and retrieval tools are crucial for maximizing the utility of these archives.

Purpose of the Study:

  • To introduce Chart Builder, an interactive, web-based platform for visualizing cryoEM and 3DEM metadata.
  • To provide researchers with a user-friendly tool for creating customizable, publication-quality visualizations from archival data.

Main Methods:

  • Chart Builder utilizes a Solr search system for flexible data querying, similar to EMDB search.
  • The platform supports various chart types (e.g., scatter, bar, line, Venn diagrams) with customizable axes and statistical operators.
  • Interactive filtering, grouping, and comparison of data are enabled without requiring programming expertise.

Main Results:

  • Researchers can create diverse, publication-quality visualizations directly from EMDB and EMPIAR metadata.
  • Data points in visualizations are linked to underlying datasets, facilitating direct access and inspection.
  • Export options include HTML embedding, persistent URLs, and data downloads, enhancing data sharing and reusability.

Conclusions:

  • Chart Builder empowers both computational and experimental researchers to explore and visualize 3DEM metadata interactively.
  • The platform promotes community-driven data analysis and aids in identifying trends within the biological 3DEM field.
  • Freely accessible and integrated into the EMDB website, Chart Builder enhances data findability, accessibility, interoperability, and reusability (FAIR principles).