Fehri, H, Gooya, A, Lu, Y et al. (3 more authors) (2019) Bayesian Polytrees With Learned Deep Features for Multi-Class Cell Segmentation. IEEE transactions on image processing : a publication of the IEEE Signal Processing Society, 28 (7). pp. 3246-3260. ISSN 1057-7149
Abstract
The recognition of different cell compartments, the types of cells, and their interactions is a critical aspect of quantitative cell biology. However, automating this problem has proven to be non-trivial and requires solving multi-class image segmentation tasks that are challenging owing to the high similarity of objects from different classes and irregularly shaped structures. To alleviate this, graphical models are useful due to their ability to make use of prior knowledge and model inter-class dependences. Directed acyclic graphs, such as trees, have been widely used to model top-down statistical dependences as a prior for improved image segmentation. However, using trees, a few inter-class constraints can be captured. To overcome this limitation, we propose polytree graphical models that capture label proximity relations more naturally compared to tree-based approaches. A novel recursive mechanism based on two-pass message passing was developed to efficiently calculate closed-form posteriors of graph nodes on polytrees. The algorithm is evaluated on simulated data and on two publicly available fluorescence microscopy datasets, outperforming directed trees and three state-of-the-art convolutional neural networks, namely, SegNet, DeepLab, and PSPNet. Polytrees are shown to outperform directed trees in predicting segmentation error by highlighting areas in the segmented image that do not comply with prior knowledge. This paves the way to uncertainty measures on the resulting segmentation and guide subsequent segmentation refinement.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © 2019 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works. |
Dates: |
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Institution: | The University of Leeds |
Academic Units: | The University of Leeds > Faculty of Engineering & Physical Sciences (Leeds) > School of Computing (Leeds) |
Depositing User: | Symplectic Publications |
Date Deposited: | 13 Jun 2019 12:09 |
Last Modified: | 13 Jun 2019 12:09 |
Status: | Published |
Publisher: | Institute of Electrical and Electronics Engineers |
Identification Number: | 10.1109/tip.2019.2895455 |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:147231 |