{"id":21318891,"url":"https://github.com/sydney-informatics-hub/microscopy-segmentation","last_synced_at":"2025-07-26T00:17:30.471Z","repository":{"id":230994403,"uuid":"636502586","full_name":"Sydney-Informatics-Hub/Microscopy-Segmentation","owner":"Sydney-Informatics-Hub","description":"Electron Microscopy Segmentation - SMM Colab Pilot Study","archived":false,"fork":false,"pushed_at":"2024-04-02T01:02:43.000Z","size":100111,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":6,"default_branch":"main","last_synced_at":"2025-03-15T22:15:14.737Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","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/Sydney-Informatics-Hub.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,"dei":null}},"created_at":"2023-05-05T01:57:57.000Z","updated_at":"2023-12-20T00:43:18.000Z","dependencies_parsed_at":"2024-04-02T02:34:32.119Z","dependency_job_id":null,"html_url":"https://github.com/Sydney-Informatics-Hub/Microscopy-Segmentation","commit_stats":null,"previous_names":["sydney-informatics-hub/microscopy-segmentation"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/Sydney-Informatics-Hub/Microscopy-Segmentation","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sydney-Informatics-Hub%2FMicroscopy-Segmentation","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sydney-Informatics-Hub%2FMicroscopy-Segmentation/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sydney-Informatics-Hub%2FMicroscopy-Segmentation/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sydney-Informatics-Hub%2FMicroscopy-Segmentation/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Sydney-Informatics-Hub","download_url":"https://codeload.github.com/Sydney-Informatics-Hub/Microscopy-Segmentation/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sydney-Informatics-Hub%2FMicroscopy-Segmentation/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":267092775,"owners_count":24034842,"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","status":"online","status_checked_at":"2025-07-25T02:00:09.625Z","response_time":70,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":[],"created_at":"2024-11-21T19:25:57.410Z","updated_at":"2025-07-26T00:17:30.371Z","avatar_url":"https://github.com/Sydney-Informatics-Hub.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Microscopy-Segmentation\nAI-assisted labeling tools and segmentation models for Electron Microscopy.\n\n![cell_segmentation](https://github.com/Sydney-Informatics-Hub/Microscopy-Segmentation/assets/20785842/eb847420-a9d3-4ded-aa40-8dc3951e2de9)\n\n## Introduction\n\nThis project aims to explore the use of computer vision AI applications to aide in imaging data downstream processing. The project focuses on electron microscopy data and explores the use of AI to assist in segmentation and annotation of data.\n\nThe main challenges are:\n- Large volumes of electron microscopy data are constantly generated, but segmentation and annotation of data is currently very time consuming and laborious.\n- Current processing tools are not well suited to electron microscopy data.\n- 2D slices of images are often not aligned, and manual alignment is time consuming and error prone.\n\n## Project Partners:\n\n- SMM and the broader Microscopy Australia\n\n## Attribution and Acknowledgement\n\nAcknowledgments are an important way for us to demonstrate the value we bring to your research. 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