Evidence map›Paper›PMID 41260214›Full record

ArticleCell reports methods2025

Temporal reassignment and correspondence evaluation with quality control for time-course imaging of 3D cell culture.

Eric M Cramer, Tamara Lopez-Vidal, Jeanette Johnson, Vania Wang, Daniel R Bergman, Ashani Weeraratna, Richard Burkhart, Elana J Fertig, Jacquelyn W Zimmerman, Laura M Heiser and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell reports methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

11 authors.

Eric M CramerDepartment of Biomedical Engineering, Oregon Health & Science University (OHSU), Portland, OR, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
Tamara Lopez-VidalDepartment of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Jeanette JohnsonDepartment of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
Vania WangDepartment of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
Daniel R BergmanDepartment of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Pharmacology and Physiology, University of Maryland School of Medicine, Baltimore, MD, USA; University of Maryland - Institute for Health Computing, University of Maryland School of Medicine, North Bethesda, MD, USA.
Ashani WeeraratnaDepartment of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
Richard BurkhartDepartment of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Elana J FertigDepartment of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; University of Maryland - Institute for Health Computing, University of Maryland School of Medicine, North Bethesda, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA; Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA.
Jacquelyn W ZimmermanDepartment of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Laura M HeiserDepartment of Biomedical Engineering, Oregon Health & Science University (OHSU), Portland, OR, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
Young Hwan ChangDepartment of Biomedical Engineering, Oregon Health & Science University (OHSU), Portland, OR, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA. Electronic address: chanyo@ohsu.edu.

Funding

Medical Scientist Training Program of Oregon Health & Science UniversityT32GM141938 · NIGMS · OREGON HEALTH & SCIENCE UNIVERSITY · PI CHEN, YABING · 2021 to 2025
$4.6M
T32: Predoctoral and Postdoctoral Training Program in Nanotechnology for Cancer ResearchT32CA153952 · NCI · JOHNS HOPKINS UNIVERSITY · PI Denis Wirtz · 2015 to 2026
$3.5M
Informing mechanistic rules of agent-based models with single-cell multi-omicsU24CA284156 · NCI · TRUSTEES OF INDIANA UNIVERSITY · PI Elana Fertig, Paul T Macklin · 2024 to 2026
$2.3M
Integrated Training in Quantitative and Experimental Cancer Systems BiologyT32CA254888 · NCI · OREGON HEALTH & SCIENCE UNIVERSITY · PI Sudarshan Anand, LISA M COUSSENS · 2021 to 2026
$2.2M
High Performance Computing and Machine Learning Infrastructure for Oregon Life SciencesS10OD034224 · OD · OREGON HEALTH & SCIENCE UNIVERSITY · PI ELLROTT, KYLE · 2023 to 2023
$2.0M
NCI NIH HHS T32 CA153952NCI NIH HHS T32 CA254888NCI NIH HHS U24 CA284156NIGMS NIH HHS T32 GM141938NIH HHS S10 OD034224
6 · The paper itself

Abstract

Longitudinal imaging of 3D cell cultures like tumor organoids and spheroids offers crucial insights into cancer progression and treatment. However, spatial displacement during time-course imaging, caused by matrix detachment or experimental artifacts, can confound analyses. We present TRACE-QC, an application of the Procrustes technique to evaluate data integrity and rectify mislabeling in longitudinal imaging of 3D cell culture. Our algorithm integrates permutation-based optimization with Procrustes analysis. By using X and Y coordinates of images, it accurately reorders, matches, and aligns object positions across time points, correcting for global well rotations and translations, along with local spheroid movements. Validation with simulated data confirmed its accuracy and robustness. Applied to longitudinal imaging of tumor spheroids, our algorithm revealed frequent displacement among the spheroids between time points and corrected many mislabeled images. This computationally efficient and adaptable method needs no experimental adjustments and presents a readily accessible solution for data quality control.

Indexed as

Cell Culture Techniques, Three DimensionalImage Processing, Computer-AssistedImaging, Three-DimensionalAlgorithmsHumansQuality ControlSpheroids, CellularTime Factors3D cell culturecancerCP: imagingextracellular matriximagingorganoidProcrustesquality controlspheroidtumor

Identifiers

PMID41260214
PMCPMC12859480

What OpenQuestion holds

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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.