Abstract
Automatic identification and segmentation of the neurons of C. elegans enables evaluating nervous system mutations, positional variability, and allows us to conduct high-throughput population studies employing many animals. A recently introduced transgene of C. elegans, named “NeuroPAL” has enabled the efficient annotation of neurons and the construction of a statistical atlas of their positions. Previous atlas-based segmentation approaches have modeled images of cells as a mixture model. The expectation-maximization (EM) algorithm and its variants are used to find the (local) maximum likelihood parameters for this class of models. We present a variation of the EM algorithm called Sinkhorn-EM (sEM) that uses regularized optimal transport Sinkhorn iterations to enforce constraints on the marginals of the joint distribution of observed variables and latent assignments in order to incorporate our prior information about cell sizes into the cluster-data assignment proportions. We apply our method to the problem of segmenting and labeling neurons in fluorescent microscopy images of C. elegans specimens. We show empirically that sEM outperforms vanilla EM and a recently proposed 3-step (filter, detect, identify) labeling approach. Open source code implementing this method is available at https://github.com/amin-nejat/SinkhornEM.
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Notes
- 1.
We add the term “vanilla” to disambiguate the standard EM meta-algorithm from the proposed variant described later in the text.
References
Aerni, S.J., et al.: Automated cellular annotation for high-resolution images of adult caenorhabditis elegans. Bioinformatics (Oxford, Engl.) 29(13), i18–i26 (2013). 23812982[pmid]
Archambeau, C., Lee, J.A., Verleysen, M., et al.: On convergence problems of the em algorithm for finite Gaussian mixtures. In: ESANN, vol. 3, pp. 99–106 (2003)
Besl, P.J., McKay, N.D.: Method for registration of 3-d shapes. In: Sensor fusion IV: control paradigms and data structures, vol. 1611, pp. 586–606. International Society for Optics and Photonics (1992)
Bubnis, G., Ban, S., DiFranco, M.D., Kato, S.: A probabilistic atlas for cell identification. arXiv:1903.09227 (2019)
Chaudhary, S., Lee, S.A., Li, Y., Patel, D.S., Lu, H.: Automated annotation of cell identities in dense cellular images. bioRxiv (2020)
Dempster, A.P., Laird, N.M., Rubin, D.B.: Maximum likelihood from incomplete data via the EM algorithm. J. Roy. Stat. Soc.: Ser. B (Methodol.) 39(1), 1–22 (1977)
Hirose, O., Kawaguchi, S., et al.: SPF-CellTracker: tracking multiple cells with strongly-correlated moves using a spatial particle filter. IEEE/ACM Trans. Comput. Biol. Bioinf. 15(6), 1822–1831 (2018)
Mena, G., Nejatbakhsh, A., Varol, E., Niles-Weed, J.: Sinkhorn EM: an expectation-maximization algorithm based on entropic optimal transport. arXiv:2006.16548 (2020)
Qu, L., et al.: Simultaneous recognition and segmentation of cells: application in C. elegans. Bioinformatics (Oxford, Engl.) 27(20), 2895–2902 (2011). 21849395[pmid]
Schrödel, T., Prevedel, R., Aumayr, K., Zimmer, M., Vaziri, A.: Brain-wide 3d imaging of neuronal activity in caenorhabditis elegans with sculpted light. Nat. Methods 10(10), 1013 (2013)
Sinkhorn, R., Knopp, P.: Concerning nonnegative matrices and doubly stochastic matrices. Pac. J. Math. 21(2), 343–348 (1967)
Tokunaga, T., et al.: Automated detection and tracking of many cells by using 4d live-cell imaging data. Bioinformatics (Oxford, Engl.) 30(12), i43–i51 (2014). 24932004[pmid]
Toyoshima, Y., Wu, S., Kanamori, M., Sato, H., Jang, M.S., Oe, S., Murakami, Y., et al.: An annotation dataset facilitates automatic annotation of whole-brain activity imaging of C. elegans. bioRxiv (2019)
Yemini, E., et al.: NeuroPAL: a neuronal polychromatic atlas of landmarks for whole-brain imaging in C. elegans. bioRxiv (2019)
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Nejatbakhsh, A., Varol, E., Yemini, E., Hobert, O., Paninski, L. (2020). Probabilistic Joint Segmentation and Labeling of C. elegans Neurons. In: Martel, A.L., et al. Medical Image Computing and Computer Assisted Intervention – MICCAI 2020. MICCAI 2020. Lecture Notes in Computer Science(), vol 12265. Springer, Cham. https://doi.org/10.1007/978-3-030-59722-1_13
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