ArticleScientific reports2018
A high-throughput imaging and nuclear segmentation analysis protocol for cleared 3D culture models.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers, 1 of them a synthesis that pooled 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.
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.
Who cites it
51 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Lung Organoids: Systematic Review of Recent Advancements and its Future Perspectives.Tissue engineering and regenerative medicine · 2024Pooled it
- High-content morphological profiling by Cell Painting in 3D spheroids.Nature communications · 2026Article
- Polyadenylation of insulin mRNA by Tent5a regulates pancreatic beta cells.Nature communications · 2026Article
- A machine learning-based analysis method for small molecule high content screening of three-dimensional cancer spheroid morphology.Molecular pharmacology · 2025Article
- In vitro biomimetic models for respiratory diseases: progress in lung organoids and lung-on-a-chip.Stem cell research & therapy · 2025Review
- Proinflammatory cytokine-induced alpha cell impairment in human islet microtissues is partially restored by dual incretin receptor agonism.Diabetologia · 2025Article
- Methylmalonic acid at the serum level in the elderly contributes to cell growth via mitochondrial dysfunction in colorectal cancer cell spheroids.Biochemistry and biophysics reports · 2025Article
- High-Throughput Single-Cell Analysis of Local Nascent Protein Deposition in 3D Microenvironments via Extracellular Protein Identification Cytometry (EPIC).Advanced materials (Deerfield Beach, Fla.) · 2025Article
- 3D-Organoid-SwinNet: High-Content Profiling of 3D Organoids.IEEE journal of biomedical and health informatics · 2025Article
- Image segmentation of treated and untreated tumor spheroids by fully convolutional networks.GigaScience · 2025Article
- Article
- Development of a human liver microphysiological coculture system for higher throughput chemical safety assessment.Toxicological sciences : an official journal of the Society of Toxicology · 2024Article
- Engineered platforms for mimicking cardiac development and drug screening.Cellular and molecular life sciences : CMLS · 2024Review
- High-throughput deconvolution of 3D organoid dynamics at cellular resolution for cancer pharmacology with Cellos.Nature communications · 2023Article
- Unbiased image segmentation assessment toolkit for quantitative differentiation of state-of-the-art algorithms and pipelines.BMC bioinformatics · 2023Article
- In-silico and in-vitro morphometric analysis of intestinal organoids.PLoS computational biology · 2023Article
- Establishment and Characterization of Free-Floating 3D Macrophage Programming Model in the Presence of Cancer Cell Spheroids.International journal of molecular sciences · 2023Article
- Applications and Advances of Multicellular Tumor Spheroids: Challenges in Their Development and Analysis.International journal of molecular sciences · 2023Review
- Subaqueous free-standing 3D cell culture system for ultrafast cell compaction, mechano-inductive immune control, and improving therapeutic angiogenesis.Bioengineering & translational medicine · 2023Article
- Scaffold-based three-dimensional cell model of pancreatic cancer is more suitable than scaffold-free three-dimensional cell model of pancreatic cancer for drug discovery.Cytotechnology · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Imaging and subsequent segmentation analysis in three-dimensional (3D) culture models are complicated by the light scattering that occurs when collecting fluorescent signal through multiple cell and extracellular matrix layers. For 3D cell culture models to be usable for drug discovery, effective and efficient imaging and analysis protocols need to be developed that enable high-throughput data acquisition and quantitative analysis of fluorescent signal. Here we report the first high-throughput protocol for optical clearing of spheroids, fluorescent high-content confocal imaging, 3D nuclear segmentation, and post-segmentation analysis. We demonstrate nuclear segmentation in multiple cell types, with accurate identification of fluorescently-labeled subpopulations, and develop a metric to assess the ability of clearing to improve nuclear segmentation deep within the tissue. Ultimately this analysis pipeline allows for previously unattainable segmentation throughput of 3D culture models due to increased sample clarity and optimized batch-processing analysis.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.