@inproceedings{fd425d38243c444da3854c926b52510a,
title = "Probabilistic Joint Segmentation and Labeling of C. elegans Neurons",
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.",
author = "Amin Nejatbakhsh and Erdem Varol and Eviatar Yemini and Oliver Hobert and Liam Paninski",
note = "Publisher Copyright: {\textcopyright} 2020, Springer Nature Switzerland AG.; 23rd International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2020 ; Conference date: 04-10-2020 Through 08-10-2020",
year = "2020",
doi = "10.1007/978-3-030-59722-1_13",
language = "English (US)",
isbn = "9783030597214",
series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",
publisher = "Springer Science and Business Media Deutschland GmbH",
pages = "130--140",
editor = "Martel, {Anne L.} and Purang Abolmaesumi and Danail Stoyanov and Diana Mateus and Zuluaga, {Maria A.} and Zhou, {S. Kevin} and Daniel Racoceanu and Leo Joskowicz",
booktitle = "Medical Image Computing and Computer Assisted Intervention – MICCAI 2020 - 23rd International Conference, Proceedings",
address = "Germany",
}