ArticleDevelopment (Cambridge, England)2019
Multi-sample SPIM image acquisition, processing and analysis of vascular growth in zebrafish.
Article in Development (Cambridge, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 52 citations in OpenAlex.
- Automated analysis of zebrafish vascular networks using the VISTA-Z pipeline.Scientific reports · 2026Article
- Technological innovations and high-throughput applications of light-sheet microscopy.Biophysics reports · 2026Article
- MIFA: Metadata, Incentives, Formats and Accessibility guidelines to improve the reuse of AI datasets for bioimage analysis.Nature methods · 2025Review
- Universal consensus 3D segmentation of cells from 2D segmented stacks.Nature methods · 2025Article
- The pericardium forms as a distinct structure during heart formation.Nature communications · 2025Article
- Imaging of cellular dynamics from a whole organism to subcellular scale with self-driving, multiscale microscopy.Nature methods · 2025Article
- Segmentation and modeling of large-scale microvascular networks: a survey.Frontiers in bioinformatics · 2025Review
- Ultrafast optical imaging techniques for exploring rapid neuronal dynamics.Neurophotonics · 2025Review
- How Tumors Affect Hemodynamics: A Diffusion Study on the Zebrafish Transplantable Model of Medullary Thyroid Carcinoma by Selective Plane Illumination Microscopy.International journal of molecular sciences · 2024Article
- Mesoscopic Oblique Plane Microscopy via Light-sheet Mirroring.bioRxiv : the preprint server for biology · 2023Article
- Exploring the dynamics of vascular adaptation.eLife · 2023Article
- Light-sheets and smart microscopy, an exciting future is dawning.Communications biology · 2023Review
- Vein fate determined by flow-based but time-delayed integration of network architecture.eLife · 2023Article
- Three-dimensional cerebral vasculature topological parameter extraction of transgenic zebrafish embryos with a filling-enhancement deep learning network.Biomedical optics express · 2023Article
- Article
- Modeling Lung Carcinoids with Zebrafish Tumor Xenograft.International journal of molecular sciences · 2022Article
- Optimized U-Net model for 3D light-sheet image segmentation of zebrafish trunk vessels.Biomedical optics express · 2022Article
- Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma.Nature communications · 2022Article
- Zebrafish vascular quantification: a tool for quantification of three-dimensional zebrafish cerebrovascular architecture by automated image analysis.Development (Cambridge, England) · 2022Article
- A Model of Discovery: The Role of Imaging Established and Emerging Non-mammalian Models in Neuroscience.Frontiers in molecular neuroscience · 2022Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To quantitatively understand biological processes that occur over many hours or days, it is desirable to image multiple samples simultaneously, and automatically process and analyse the resulting datasets. Here, we present a complete multi-sample preparation, imaging, processing and analysis workflow to determine the development of the vascular volume in zebrafish. Up to five live embryos were mounted and imaged simultaneously over several days using selective plane illumination microscopy (SPIM). The resulting large imagery dataset of several terabytes was processed in an automated manner on a high-performance computer cluster and segmented using a novel segmentation approach that uses images of red blood cells as training data. This analysis yielded a precise quantification of growth characteristics of the whole vascular network, head vasculature and tail vasculature over development. Our multi-sample platform demonstrates effective upgrades to conventional single-sample imaging platforms and paves the way for diverse quantitative long-term imaging studies.
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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.