ArticleScientific reports2023
SproutAngio: an open-source bioimage informatics tool for quantitative analysis of sprouting angiogenesis and lumen space.
Article in Scientific reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 15 citations in OpenAlex.
- Linking preclinical models with functional imaging and artificial intelligence to decode tumor angiogenesis.Pharmacological reports : PR · 2026Review
- Clinically approved HIF-PHIs modulate redox metabolism, cell growth, and angiogenesis independent of HIF-1α/HIF-2α.Redox biology · 2026Article
- VASCilia is an open-source, deep learning-based tool for 3D analysis of cochlear hair cell stereocilia bundles.PLoS biology · 2026Article
- VESNA: an open-source tool for automated 3D vessel segmentation and network analysis.BMC bioinformatics · 2025Article
- A graph-theoretic framework for quantitative analysis of angiogenic networks.BioData mining · 2025Article
- VASCilia (Vision Analysis StereoCilia): A Napari Plugin for Deep Learning-Based 3D Analysis of Cochlear Hair Cell Stereocilia Bundles.bioRxiv : the preprint server for biology · 2025Article
- Falsifying computational models of endothelial cell network formation through quantitative comparison with in vitro models.PLoS computational biology · 2025Article
- Epigenetic drug screening identifies enzyme inhibitors A-196 and TMP-269 as novel regulators of sprouting angiogenesis.Scientific reports · 2025Article
- Integrating Vascular Phenotypic and Proteomic Analysis in an Open Microfluidic Platform.ACS nano · 2024Article
- Long-term day-by-day tracking of microvascular networks sprouting in fibrin gels: From detailed morphological analyses to general growth rules.APL bioengineering · 2024Article
- A Comprehensive Look at In Vitro Angiogenesis Image Analysis Software.International journal of molecular sciences · 2023Review
- ErbB signaling is a potential therapeutic target for vascular lesions with fibrous component.eLife · 2023Article
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Authors and funding
9 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Three-dimensional image analyses are required to improve the understanding of the regulation of blood vessel formation and heterogeneity. Currently, quantitation of 3D endothelial structures or vessel branches is often based on 2D projections of the images losing their volumetric information. Here, we developed SproutAngio, a Python-based open-source tool, for fully automated 3D segmentation and analysis of endothelial lumen space and sprout morphology. To test the SproutAngio, we produced a publicly available in vitro fibrin bead assay dataset with a gradually increasing VEGF-A concentration ( https://doi.org/10.5281/zenodo.7240927 ). We demonstrate that our automated segmentation and sprout morphology analysis, including sprout number, length, and nuclei number, outperform the widely used ImageJ plugin. We also show that SproutAngio allows a more detailed and automated analysis of the mouse retinal vasculature in comparison to the commonly used radial expansion measurement. In addition, we provide two novel methods for automated analysis of endothelial lumen space: (1) width measurement from tip, stalk and root segments of the sprouts and (2) paired nuclei distance analysis. We show that these automated methods provided important additional information on the endothelial cell organization in the sprouts. The pipelines and source code of SproutAngio are publicly available ( https://doi.org/10.5281/zenodo.7381732 ).
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