Evidence map›Paper›PMID 40875368›Full record

ArticleMolecular biology of the cell2025

Automated segmentation of soft X-ray tomography: Native cellular structure with submicron resolution at high-throughput for whole-cell quantitative imaging in yeast.

Jianhua Chen, Mary Mirvis, Axel Ekman, Bieke Vanslembrouck, Mark Le Gros, Carolyn Larabell, Wallace F Marshall

Abstract read
In one paragraph

Article in Molecular biology of the cell, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
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

4 citing papers in PubMed.

  1. Article
  2. Article
  3. Optimal disk packing of chloroplasts in plant cells.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  4. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

7 authors.

Jianhua ChenNational Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
Mary MirvisDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158.ORCID 0000-0003-2839-7719
Axel EkmanNational Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
Bieke VanslembrouckNational Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
Mark Le GrosNational Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
Carolyn LarabellNational Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
Wallace F MarshallDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158.

Funding

Origins of Cell GeometryR35GM130327 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Wallace Marshall · 2019 to 2026
$5.3M
User Training and OutreachP30GM138441 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI LARABELL, CAROLYN A · 2020 to 2023
$3.7M
NIGMS NIH HHS P30 GM138441NIGMS NIH HHS R35 GM130327
6 · The paper itself

Abstract

Soft X-ray tomography (SXT) is an invaluable tool for quantitatively analyzing cellular structures at suboptical isotropic resolution. However, it has traditionally depended on manual segmentation, limiting its scalability for large datasets. Here, we leverage a deep learning-based autosegmentation pipeline to segment and label cellular structures in hundreds of cells across three

Indexed as

Saccharomyces cerevisiaeTomography, X-RayDeep LearningImage Processing, Computer-AssistedImaging, Three-DimensionalOrganelles

Identifiers

PMID40875368
PMCPMC12509287

What Socratic 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 Socratic graph.