{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/wormpose-image-synthesis-and-convolutional","title":"WormPose: Image synthesis and convolutional networks for pose estimation in C. elegans","arxiv_id":null,"date":"2020-07-10","proceeding":"Plos Computational Biology 2021 4","authors":["Laetitia Hebert","Tosif Ahamed","Antonio C Costa","Liam O'Shaughnessy","Greg J. Stephens"],"abstract":"An important model system for understanding genes, neurons and behavior, the nematode worm C. elegans naturally moves through a variety of complex postures, for which estimation from video data is challenging. We introduce an open-source Python package, WormPose, for 2D pose estimation in C. elegans , including self-occluded, coiled shapes. We leverage advances in machine vision afforded from convolutional neural networks and introduce a synthetic yet realistic generative model for images of worm posture, thus avoiding the need for human-labeled training. WormPose is effective and adaptable for imaging conditions across worm tracking efforts. We quantify pose estimation using synthetic data as well as N2 and mutant worms in on-food conditions. We further demonstrate WormPose by analyzing long (~10 hour), fast-sampled (~30 Hz) recordings of on-food N2 worms to provide a posture-scale analysis of roaming/dwelling behaviors.","url_abs":"https://www.biorxiv.org/content/10.1101/2020.07.09.193755v1","url_pdf":"https://www.biorxiv.org/content/10.1101/2020.07.09.193755v1.full.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"wormpose-image-synthesis-and-convolutional","repo_url":"https://github.com/iteal/wormpose","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[{"task_slug":"2d-pose-estimation","task_name":"2D Pose Estimation"},{"task_slug":"animal-pose-estimation","task_name":"Animal Pose Estimation"},{"task_slug":"image-generation","task_name":"Image Generation"},{"task_slug":"pose-estimation","task_name":"Pose Estimation"}],"methods":[{"method_slug":"1x1-convolution","method_name":"1x1 Convolution"},{"method_slug":"adam","method_name":"Adam"},{"method_slug":"average-pooling","method_name":"Average Pooling"},{"method_slug":"batch-normalization","method_name":"Batch Normalization"},{"method_slug":"bottleneck-residual-block","method_name":"Bottleneck Residual Block"},{"method_slug":"convolution","method_name":"Convolution"},{"method_slug":"global-average-pooling","method_name":"Global Average Pooling"},{"method_slug":"kaiming-initialization","method_name":"Kaiming Initialization"},{"method_slug":"max-pooling","method_name":"Max Pooling"},{"method_slug":"relu","method_name":"ReLU"},{"method_slug":"residual-block","method_name":"Residual Block"},{"method_slug":"residual-connection","method_name":"Residual Connection"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}