Evidence map›Paper›PMID 40247123›Full record

ReviewNature methods2025

Imaging 3D cell cultures with optical microscopy.

Huai-Ching Hsieh, Qinghua Han, David Brenes, Kevin W Bishop, Rui Wang, Yuli Wang, Chetan Poudel, Adam K Glaser, Benjamin S Freedman, Joshua C Vaughan and 2 more

Abstract readReview
In one paragraph

Review in Nature methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing 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

8 citing papers in PubMed.

  1. Review
  2. Review
  3. Article
  4. Article
  5. Review
  6. Review
  7. An Intelligent Magneto-Mechanical Platform for Cellular Sensing in 3D Microenvironments.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026
    Article
  8. Review
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

12 authors.

Huai-Ching HsiehDepartment of Bioengineering, University of Washington, Seattle, WA, USA.
Qinghua HanDepartment of Bioengineering, University of Washington, Seattle, WA, USA.
David BrenesDepartment of Mechanical Engineering, University of Washington, Seattle, WA, USA.
Kevin W BishopDepartment of Bioengineering, University of Washington, Seattle, WA, USA.ORCID http://orcid.org/0000-0001-8722-6464
Rui WangDepartment of Mechanical Engineering, University of Washington, Seattle, WA, USA.ORCID http://orcid.org/0009-0007-6553-2074
Yuli WangDepartment of Bioengineering, University of Washington, Seattle, WA, USA.
Chetan PoudelDepartment of Chemistry, University of Washington, Seattle, WA, USA.
Adam K GlaserAllen Institute for Neural Dynamics, Seattle, WA, USA.
Benjamin S FreedmanDepartment of Bioengineering, University of Washington, Seattle, WA, USA.ORCID http://orcid.org/0000-0003-2228-7383
Joshua C VaughanDepartment of Chemistry, University of Washington, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-6550-8935
Nancy L AllbrittonDepartment of Bioengineering, University of Washington, Seattle, WA, USA.
Jonathan T C LiuDepartment of Bioengineering, University of Washington, Seattle, WA, USA. jonliu@uw.edu.ORCID http://orcid.org/0000-0001-5650-3086

Funding

Translational center for kidney microphysiological systems to improve drug safety and efficacyU2CTR004867 · NCATS · UNIVERSITY OF WASHINGTON · PI Benjamin Solomon Freedman, Jonathan Himmelfarb · 2024 to 2026
$4.8M
Resource Development CoreU54DK137328 · NIDDK · INDIANA UNIVERSITY INDIANAPOLIS · PI Pierre C Dagher · 2023 to 2026
$4.5M
Cell specific delivery of novel therapies to enhance glomerular regeneration and repairUC2DK126006 · NIDDK · UNIVERSITY OF WASHINGTON · PI SHANKLAND, STUART JAMES · 2020 to 2024
$4.0M
Prostate cancer risk stratification via computational 3D pathologyR01CA268207 · NCI · UNIVERSITY OF WASHINGTON · PI Jonathan T.C. Liu, Anant Madabhushi · 2022 to 2026
$3.1M
Development of a microphysiologic system to assay the interaction of the human colonic epithelium on Clostridium difficileR01DK120606 · NIDDK · UNIVERSITY OF WASHINGTON · PI ALLBRITTON, NANCY L., SHEIKH, SHEHZAD Z. · 2020 to 2023
$2.2M
SCGE Comparative Studies SupplementU01DK127553 · NIDDK · UNIVERSITY OF WASHINGTON · PI FREEDMAN, BENJAMIN SOLOMON · 2020 to 2022
$2.2M
Computational 3D pathology for Barrett's esophagus risk stratificationR01DK138948 · NIDDK · UNIVERSITY OF WASHINGTON · PI William Mallory Grady, Jonathan T.C. Liu · 2024 to 2026
$2.2M
Instrumentation platform for 3D pathology with open-top light-sheet microscopyR01EB031002 · NIBIB · UNIVERSITY OF WASHINGTON · PI LIU, JONATHAN T.C. · 2021 to 2024
$1.9M
Targeting Myosin to Treat Polycystic Kidney DiseaseR42DK136452 · NIDDK · PLUREXA LLC · PI Benjamin Solomon Freedman · 2025 to 2026
$1.6M
Utility of Human Organoids for Safety and Efficiency Evaluations of Genome Editing TherapeuticsU01AI176460 · NIAID · UNIVERSITY OF WASHINGTON · PI FREEDMAN, BENJAMIN SOLOMON · 2023 to 2025
$1.0M
Light-sheet micro-aspiration microscopy for the isolation and analysis of rare tumor cells from intact clinical specimensR00CA240681 · NCI · ALLEN INSTITUTE · PI GLASER, ADAM K · 2021 to 2023
$745k
NCATS NIH HHS U2C TR004867NCI NIH HHS R00 CA240681NCI NIH HHS R01 CA268207NIAID NIH HHS U01 AI176460NIBIB NIH HHS R01 EB031002NIDDK NIH HHS R01 DK120606NIDDK NIH HHS R01 DK138948NIDDK NIH HHS R42 DK136452NIDDK NIH HHS U01 DK127553NIDDK NIH HHS U54 DK137328NIDDK NIH HHS UC2 DK126006U.S. Department of Defense (United States Department of Defense) W81XWH-20-1-0851U.S. Department of Health & Human Services | National Institutes of Health (NIH) R00CA240681U.S. Department of Health & Human Services | National Institutes of Health (NIH) R01CA268207U.S. Department of Health & Human Services | National Institutes of Health (NIH) R01DK120606U.S. Department of Health & Human Services | National Institutes of Health (NIH) R01DK138948U.S. Department of Health & Human Services | National Institutes of Health (NIH) U01AI176460U.S. Department of Health & Human Services | National Institutes of Health (NIH) U01DK127553U.S. Department of Health & Human Services | National Institutes of Health (NIH) U2CTR004867U.S. Department of Health & Human Services | National Institutes of Health (NIH) U54DK137328U.S. Department of Health & Human Services | National Institutes of Health (NIH) UC2DK126006
6 · The paper itself

Abstract

Three-dimensional (3D) cell cultures have gained popularity in recent years due to their ability to represent complex tissues or organs more faithfully than conventional two-dimensional (2D) cell culture. This article reviews the application of both 2D and 3D microscopy approaches for monitoring and studying 3D cell cultures. We first summarize the most popular optical microscopy methods that have been used with 3D cell cultures. We then discuss the general advantages and disadvantages of various microscopy techniques for several broad categories of investigation involving 3D cell cultures. Finally, we provide perspectives on key areas of technical need in which there are clear opportunities for innovation. Our goal is to guide microscope engineers and biomedical end users toward optimal imaging methods for specific investigational scenarios and to identify use cases in which additional innovations in high-resolution imaging could be helpful.

Indexed as

Cell Culture Techniques, Three DimensionalImaging, Three-DimensionalMicroscopyAnimalsHumans

Identifiers

PMID40247123
PMCPMC12402705

What OpenQuestion holds

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Registered trials

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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.