Automated Segmentation of HeLa Nuclear Envelope from Electron Microscopy Images View Full Text


Ontology type: schema:Chapter      Open Access: True


Chapter Info

DATE

2018

AUTHORS

Cefa Karabağ , Martin L. Jones , Christopher J. Peddie , Anne E. Weston , Lucy M. Collinson , Constantino Carlos Reyes-Aldasoro

ABSTRACT

This paper describes an image-processing pipeline for the automatic segmentation of the nuclear envelope of HeLa cells 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 hand-segmented 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 s 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. More... »

PAGES

241-250

References to SciGraph publications

Book

TITLE

Medical Image Understanding and Analysis

ISBN

978-3-319-95920-7
978-3-319-95921-4

From Grant

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/978-3-319-95921-4_23

DOI

http://dx.doi.org/10.1007/978-3-319-95921-4_23

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1106254307


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