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Automated Segmentation of HeLa Nuclear Envelope from Electron Microscopy Images

Karabag, C., Jones, M. L., Peddie, C. J., Weston, A. E., Collinson, L. M. and Reyes-Aldasoro, C. C. ORCID: 0000-0002-9466-2018 (2018). Automated Segmentation of HeLa Nuclear Envelope from Electron Microscopy Images. Communications in Computer and Information Science, doi: 10.1007/978-3-319-95921-4_23

Abstract

This paper describes an image-processing pipeline for the automatic segmentation of the nuclear envelope of HeLcells observed through Electron Microscopy. The pipeline was applied to a 3D stack of 300 images. The intermediate results of neighbouring slices are further combined to improve the final results. Comparison with a handsegmented ground truth reported Jaccard similarity values between 94-98% on the central slices with a decrease towards the edges of the cell where the structure was considerably more complex. The processing is unsupervised and each 2D slice is processed in about 5-10 seconds running on a MacBook Pro. No systematic attempt to make the code faster was made. These encouraging results could be further used to provide data for more complex segmentation techniques like Deep Learning, which require a considerable amount of data to train architectures like Convolutional Neural Networks. The code is freely available from https://github.com/reyesaldasoro/HeLa-Cell-Segmentation

Publication Type: Article
Additional Information: The final authenticated version is to be available online at https://doi.org/10.1007/978-3-319-95921-4_23
Subjects: T Technology > TK Electrical engineering. Electronics Nuclear engineering
Departments: School of Mathematics, Computer Science & Engineering > Engineering
School of Mathematics, Computer Science & Engineering > Engineering > Electrical & Electronic Engineering
URI: http://openaccess.city.ac.uk/id/eprint/19564
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