ArticleStem cell reports2014
A rapid and efficient 2D/3D nuclear segmentation method for analysis of early mouse embryo and stem cell image data.
Article in Stem cell reports, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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Who cites it
65 citing papers in PubMed.
- Systematic evaluation of computational methods for cell segmentation.Briefings in bioinformatics · 2026Article
- Wnt/β-catenin signalling modulates the timing of cell fate decision making in the early mouse embryo.PloS one · 2026Article
- Donor embryonic stem cells displace host cells of 8-cell-stage chimeras to the extra-embryonic lineages by spatial crowding and FGF4 signalling.Development (Cambridge, England) · 2025Article
- ETV4 and ETV5 orchestrate FGF-mediated lineage specification and epiblast maturation during early mouse development.Development (Cambridge, England) · 2025Article
- Nuclear instance segmentation and tracking for preimplantation mouse embryos.Development (Cambridge, England) · 2024Article
- Two-dimensional segmentation fusion tool: an extensible, free-to-use, user-friendly tool for combining different bidimensional segmentations.Frontiers in bioengineering and biotechnology · 2024Article
- The salt-and-pepper pattern in mouse blastocysts is compatible with signaling beyond the nearest neighbors.iScience · 2023Article
- insideOutside: an accessible algorithm for classifying interior and exterior points, with applications in embryology.Biology open · 2023Article
- Plpp3, a novel regulator of pluripotency exit and endodermal differentiation of mouse embryonic stem cells.Biology open · 2023Article
- A comprehensive review of computational and image analysis techniques for quantitative evaluation of striated muscle tissue architecture.Biophysics reviews · 2022Review
- Discovery of Highly Functionalized 5-hydroxy-2Cancers · 2022Article
- Artificial-Intelligence-Based Imaging Analysis of Stem Cells: A Systematic Scoping Review.Biology · 2022Article
- RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription.Genes & development · 2022Article
- Marker-controlled watershed with deep edge emphasis and optimized H-minima transform for automatic segmentation of densely cultivated 3D cell nuclei.BMC bioinformatics · 2022Article
- GIANI - open-source software for automated analysis of 3D microscopy images.Journal of cell science · 2022Article
- Rapid and efficient degradation of endogenous proteins in vivo identifies stage-specific roles of RNA Pol II pausing in mammalian development.Developmental cell · 2022Article
- Evaluating Autophagy in Preimplantation Embryos.Autophagy reports · 2022Review
- Imaging developmental cell cycles.Biophysical journal · 2021Review
- IVEN: A quantitative tool to describe 3D cell position and neighbourhood reveals architectural changes in FGF4-treated preimplantation embryos.PLoS biology · 2021Article
- Deep neural net tracking of human pluripotent stem cells reveals intrinsic behaviors directing morphogenesis.Stem cell reports · 2021Article
5 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
Segmentation is a fundamental problem that dominates the success of microscopic image analysis. In almost 25 years of cell detection software development, there is still no single piece of commercial software that works well in practice when applied to early mouse embryo or stem cell image data. To address this need, we developed MINS (modular interactive nuclear segmentation) as a MATLAB/C++-based segmentation tool tailored for counting cells and fluorescent intensity measurements of 2D and 3D image data. Our aim was to develop a tool that is accurate and efficient yet straightforward and user friendly. The MINS pipeline comprises three major cascaded modules: detection, segmentation, and cell position classification. An extensive evaluation of MINS on both 2D and 3D images, and comparison to related tools, reveals improvements in segmentation accuracy and usability. Thus, its accuracy and ease of use will allow MINS to be implemented for routine single-cell-level image analyses.
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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.