{"id":13592853,"url":"https://github.com/tarolangner/ukb_segmentation","last_synced_at":"2025-04-09T02:31:28.607Z","repository":{"id":41107705,"uuid":"303342446","full_name":"tarolangner/ukb_segmentation","owner":"tarolangner","description":"PyTorch implementation for 2.5D U-Net segmentation of UK Biobank neck-to-knee body MRI","archived":false,"fork":false,"pushed_at":"2023-02-10T16:42:07.000Z","size":450,"stargazers_count":17,"open_issues_count":0,"forks_count":3,"subscribers_count":4,"default_branch":"main","last_synced_at":"2024-11-06T14:40:03.414Z","etag":null,"topics":["deep-learning","kidney","mri","neural-networks","parenchyma","pytorch","segmentation","semantic-segmentation","u-net","uk-biobank"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/tarolangner.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null}},"created_at":"2020-10-12T09:29:03.000Z","updated_at":"2024-10-11T06:00:19.000Z","dependencies_parsed_at":"2024-01-16T22:20:08.474Z","dependency_job_id":"ab875626-8856-4ae7-9689-cc945274b1cc","html_url":"https://github.com/tarolangner/ukb_segmentation","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tarolangner%2Fukb_segmentation","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tarolangner%2Fukb_segmentation/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tarolangner%2Fukb_segmentation/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tarolangner%2Fukb_segmentation/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/tarolangner","download_url":"https://codeload.github.com/tarolangner/ukb_segmentation/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247965514,"owners_count":21025393,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["deep-learning","kidney","mri","neural-networks","parenchyma","pytorch","segmentation","semantic-segmentation","u-net","uk-biobank"],"created_at":"2024-08-01T16:01:13.968Z","updated_at":"2025-04-09T02:31:23.577Z","avatar_url":"https://github.com/tarolangner.png","language":"Python","funding_links":[],"categories":["Imaging phenotypes"],"sub_categories":["Abdominal MRI"],"readme":"# Neural networks for semantic segmentation of UK Biobank neck-to-knee body MRI\n\n![title](figures/header.png)\n\nThis repository contains PyTorch code for cross-validation and inference with neural networks for kidney segmentation on UK Biobank neck-to-knee body MRI, as described in:  \n[_\"Kidney segmentation in neck-to-knee body MRI of 40,000 UK Biobank participants\"_](https://arxiv.org/abs/2006.06996) [1]\n\nThe included inference pipeline and trained snapshot enables measurements of left and right parenchymal kidney volumes (excluding cysts and vessels) from these images.\n\nContents:\n- 2.5D U-Net architecture with residual connections (based on [TernausNet, Iglovikov et al. 2018](https://arxiv.org/pdf/1801.05746.pdf))\n- Infrastructure for training and *cross-validation*\n- Pipeline for *inference* on neck-to-knee body MRI DICOMs\n- Code for *quality_controls* based on numerical metrics\n- A [_trained snapshot for parenchymal kidney tissue can be found here_](https://uppsala.box.com/s/lan3d807uqz3rhk6vf7o8u5jjnex4jyp)\n\nFor any questions and suggestions, feel free to reach out!\n\n# Notes\nAccess to the underlying image data can only be granted by [the UK Biobank Study](https://www.ukbiobank.ac.uk/register-apply/). Annotations from the quality controls used in our work [1] are available under return data ID 2345 for our application 14237. Our measurements and annotations for the kidneys will eventually be made available as well.\n\n# Citation\nIf you use this code for any derived work, please consider citing [1] and linking this GitHub.\n\n# References\n\n[1] [_T. Langner, A. Östling, L. Maldonis, A. Karlsson, D. Olmo, D. Lindgren, A. Wallin, L. Lundin, R. Strand, H. Ahlström, J. Kullberg, “Kidney segmentation in neck-to-knee body MRI of 40,000 UK Biobank participants,” Scientific reports 10.1 (2020): 1-10_](https://www.nature.com/articles/s41598-020-77981-4)\\\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftarolangner%2Fukb_segmentation","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftarolangner%2Fukb_segmentation","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftarolangner%2Fukb_segmentation/lists"}