ArticlePLoS biology2019
Nessys: A new set of tools for the automated detection of nuclei within intact tissues and dense 3D cultures.
Article in PLoS biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- A toolkit for mapping cell identities in relation to neighbors reveals conserved patterning of neuromesodermal progenitor populations.PLoS biology · 2025Article
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- In vitro modelling of anterior primitive streak patterning with human pluripotent stem cells identifies the path to notochord progenitors.Development (Cambridge, England) · 2024Article
- Nuclear instance segmentation and tracking for preimplantation mouse embryos.Development (Cambridge, England) · 2024Article
- Enabling neighbour labelling: using synthetic biology to explore how cells influence their neighbours.Development (Cambridge, England) · 2024Review
- insideOutside: an accessible algorithm for classifying interior and exterior points, with applications in embryology.Biology open · 2023Article
- Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations.Nucleic acids research · 2023Article
- A deep learning framework for quantitative analysis of actin microridges.NPJ systems biology and applications · 2023Article
- SyNPL: Synthetic Notch pluripotent cell lines to monitor and manipulate cell interactions in vitro and in vivo.Development (Cambridge, England) · 2022Article
- GIANI - open-source software for automated analysis of 3D microscopy images.Journal of cell science · 2022Article
- Mechanical constraints to cell-cycle progression in a pseudostratified epithelium.Current biology : CB · 2022Article
- Cell-state transitions and collective cell movement generate an endoderm-like region in gastruloids.eLife · 2022Article
- Steerable Near-Quadrature Filter Pairs in Three Dimensions.SIAM journal on imaging sciences · 2022Article
- 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
- The transcription factor E2A drives neural differentiation in pluripotent cells.Development (Cambridge, England) · 2020Article
- Routine Optical Clearing of 3D-Cell Cultures: Simplicity Forward.Frontiers in molecular biosciences · 2020Article
- OpSeF: Open Source Python Framework for Collaborative Instance Segmentation of Bioimages.Frontiers in bioengineering and biotechnology · 2020Article
- N-cadherin stabilises neural identity by dampening anti-neural signals.Development (Cambridge, England) · 2019Article
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Authors and funding
6 authors.
Funding
Abstract
Methods for measuring the properties of individual cells within their native 3D environment will enable a deeper understanding of embryonic development, tissue regeneration, and tumorigenesis. However, current methods for segmenting nuclei in 3D tissues are not designed for situations in which nuclei are densely packed, nonspherical, or heterogeneous in shape, size, or texture, all of which are true of many embryonic and adult tissue types as well as in many cases for cells differentiating in culture. Here, we overcome this bottleneck by devising a novel method based on labelling the nuclear envelope (NE) and automatically distinguishing individual nuclei using a tree-structured ridge-tracing method followed by shape ranking according to a trained classifier. The method is fast and makes it possible to process images that are larger than the computer's memory. We consistently obtain accurate segmentation rates of >90%, even for challenging images such as mid-gestation embryos or 3D cultures. We provide a 3D editor and inspector for the manual curation of the segmentation results as well as a program to assess the accuracy of the segmentation. We have also generated a live reporter of the NE that can be used to track live cells in 3 dimensions over time. We use this to monitor the history of cell interactions and occurrences of neighbour exchange within cultures of pluripotent cells during differentiation. We provide these tools in an open-access user-friendly format.
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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.