bioRxivCancer BiologyPreprint
Modelling the nuclear envelope of HeLa cells
Cefa Karabağ, Martin L. JonesiD, Christopher J. PeddieiD, Anne E. Weston, Lucy M. Collinson, Constantino Carlos Reyes-AldasoroiD
Abstract
This paper describes a framework for the automatic segmentation of the nuclear envelope of cancerous HeLa cells and the modelling of the volumetric shape against an ellipsoid. The framework is automatic and unsupervised and reported a Jaccard Similarity Index of 0.968 against a manual segmentation. The modelling of the surface provides a visual display of the variations, both smooth and rugged over the surface, and measurements can be extracted with the expectation that they can correlate with the biological characteristics of the cells.
Reproducibility ledger
Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.
Sign in to file a reproducibility report.
Related papers
- Volumetric Semantic Instance Segmentation of the Plasma Membrane of HeLa Cells
C. Karabag, M. L. Jones, C. C. Reyes-Aldasoro·bioRxiv·Apr 30, 2021
- Geometric differences between nuclear envelopes of Wild-type and Chlamydia trachomatis-infected HeLa cells
C. Karabag, M. L. Jones, … C. C. Reyes-Aldasoro·bioRxiv·Apr 2, 2020
- Citizen science, cells and CNNs - deep learning for automatic segmentation of the nuclear envelope in electron microscopy data, trained with volunteer segmentations
H. Spiers, H. Songhurst, … M. L. Jones·bioRxiv·Jul 28, 2020
- Relationship Between Irregularities of the Nuclear Envelope and Mitochondria in HeLa cells Observed with Electron Microscopy
Daniel Brito-Pacheco, Cefa Karabağ, … Constantino Carlos Reyes‐Aldasoro·IEEE International Symposium on Biomedical Imaging (ISBI)Peer-reviewed·May 27, 2024
- 3D Shape Modeling for Cell Nuclear Morphological Analysis and Classification
Alexandr A. Kalinin, Ari Allyn-Feuer, … Ivo D. Dinov·Scientific ReportsPeer-reviewed·Sep 6, 2018
- Evaluation of training data, ground truth and shape variability in the semantic segmentation of HeLa cells observed with electron microscopy
C. Karabag, C. C. Reyes-Aldasoro·bioRxiv·Jun 1, 2022