Evidence map›Paper›PMID 36805107›Full record

ArticleeLife2023

Cryo-plasma FIB/SEM volume imaging of biological specimens.

Maud Dumoux, Thomas Glen, Jake L R Smith, Elaine M L Ho, Luis M A Perdigão, Avery Pennington, Sven Klumpe, Neville B Y Yee, David Andrew Farmer, Pui Y A Lai and 10 more

Open access · goldAbstract read
In one paragraph

Article in eLife, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.

0numbers the graph read from it
0cells of the map it votes in
22citing papers in PubMed
14.1field-weighted citation impact, top 2% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

22 citing papers in PubMed, 51 citations in OpenAlex.

  1. Review
  2. Review
  3. Article
  4. Review
  5. Article
  6. Review
  7. Article
  8. Structural glycobiology - from enzymes to organelles.Biochemical Society transactions · 2025
    Review
  9. Review
  10. Methods to Study Poxvirus Structures by Cryo-EM Imaging Modalities.Methods in molecular biology (Clifton, N.J.) · 2025
    Article
  11. Review
  12. Article
  13. Review
  14. Article
  15. Article
  16. Article
  17. Integrative Approaches to Study Virus Structures.Sub-cellular biochemistry · 2024
    Review
  18. Cryo-electron tomography to study viral infection.Biochemical Society transactions · 2023
    Review
  19. Review
  20. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

20 authors at 5 institutions in 3 countries.

Maud DumouxStructural Biology, Rosalind Franklin Institute, Didcot, United Kingdom.ORCID 0000-0002-1732-1041
Thomas GlenStructural Biology, Rosalind Franklin Institute, Didcot, United Kingdom.
Jake L R SmithStructural Biology, Rosalind Franklin Institute, Didcot, United Kingdom.
Elaine M L HoArtificial Intelligence and Informatics, Rosalind Franklin Institute, Didcot, United Kingdom.
Luis M A PerdigãoArtificial Intelligence and Informatics, Rosalind Franklin Institute, Didcot, United Kingdom.
Avery PenningtonDiamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom.
Sven KlumpeResearch Group Cryo-EM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany.
Neville B Y YeeArtificial Intelligence and Informatics, Rosalind Franklin Institute, Didcot, United Kingdom.ORCID 0000-0003-0349-3958
David Andrew FarmerDiamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom.ORCID 0000-0001-5331-3551
Pui Y A LaiDiamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom.
William BowlesStructural Biology, Rosalind Franklin Institute, Didcot, United Kingdom.ORCID 0000-0001-8115-4404
Ron KelleyMaterials and Structural Analysis Division, Thermo Fisher Scientific, Eindhoven, Netherlands.
Jürgen M PlitzkoResearch Group Cryo-EM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany.ORCID 0000-0002-6402-8315
Liang WuStructural Biology, Rosalind Franklin Institute, Didcot, United Kingdom.
Mark BashamDiamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom.ORCID 0000-0002-8438-1415
Daniel K ClareDiamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom.
C Alistair SiebertDiamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom.
Michele C DarrowArtificial Intelligence and Informatics, Rosalind Franklin Institute, Didcot, United Kingdom.ORCID 0000-0001-6259-1684
James H NaismithStructural Biology, Rosalind Franklin Institute, Didcot, United Kingdom.
Michael GrangeStructural Biology, Rosalind Franklin Institute, Didcot, United Kingdom.ORCID 0000-0003-2580-2299
Diamond Light Source · GBRosalind Franklin Institute · GBCentre for Human Genetics · GBMax Planck Institute of Biochemistry · DEThermo Fisher Scientific (Japan) · JP

Funding

Wellcome TrustWellcome Trust 218579/Z/19/ZWellcome Trust 220526/Z/20/Z
6 · The paper itself

Abstract

Serial focussed ion beam scanning electron microscopy (FIB/SEM) enables imaging and assessment of subcellular structures on the mesoscale (10 nm to 10 µm). When applied to vitrified samples, serial FIB/SEM is also a means to target specific structures in cells and tissues while maintaining constituents' hydration shells for in situ structural biology downstream. However, the application of serial FIB/SEM imaging of non-stained cryogenic biological samples is limited due to low contrast, curtaining, and charging artefacts. We address these challenges using a cryogenic plasma FIB/SEM. We evaluated the choice of plasma ion source and imaging regimes to produce high-quality SEM images of a range of different biological samples. Using an automated workflow we produced three-dimensional volumes of bacteria, human cells, and tissue, and calculated estimates for their resolution, typically achieving 20-50 nm. Additionally, a tag-free localisation tool for regions of interest is needed to drive the application of in situ structural biology towards tissue. The combination of serial FIB/SEM with plasma-based ion sources promises a framework for targeting specific features in bulk-frozen samples (>100 µm) to produce lamellae for cryogenic electron tomography.

Indexed as

Electron Microscope TomographyImaging, Three-DimensionalHumansIonsMicroscopy, Electron, ScanningIonscell biologyHeLa cellshumanmouse tissue (brain)mouse tissue (cardiac)R. rubrumS. cerevisiaeVero cells

Identifiers

PMID36805107
PMCPMC9995114
OpenAlexW4321453226

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.