{"id":16285692,"url":"https://github.com/abailoni/cellpose-training-gui","last_synced_at":"2026-02-05T23:01:09.058Z","repository":{"id":62832912,"uuid":"444359957","full_name":"abailoni/cellpose-training-gui","owner":"abailoni","description":"Graphical tool for creating image segmentation annotations and training custom Cellpose models","archived":false,"fork":false,"pushed_at":"2024-05-06T13:35:31.000Z","size":8649,"stargazers_count":3,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-07-11T07:26:08.171Z","etag":null,"topics":["annotation","cellpose","gui","segmentation"],"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/abailoni.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,"publiccode":null,"codemeta":null}},"created_at":"2022-01-04T09:30:34.000Z","updated_at":"2024-02-05T01:20:06.000Z","dependencies_parsed_at":"2024-10-20T19:08:52.915Z","dependency_job_id":null,"html_url":"https://github.com/abailoni/cellpose-training-gui","commit_stats":null,"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"purl":"pkg:github/abailoni/cellpose-training-gui","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/abailoni%2Fcellpose-training-gui","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/abailoni%2Fcellpose-training-gui/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/abailoni%2Fcellpose-training-gui/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/abailoni%2Fcellpose-training-gui/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/abailoni","download_url":"https://codeload.github.com/abailoni/cellpose-training-gui/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/abailoni%2Fcellpose-training-gui/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29137750,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-05T22:49:08.052Z","status":"ssl_error","status_checked_at":"2026-02-05T22:45:32.059Z","response_time":65,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["annotation","cellpose","gui","segmentation"],"created_at":"2024-10-10T19:25:40.316Z","updated_at":"2026-02-05T23:01:09.036Z","avatar_url":"https://github.com/abailoni.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Tool for Image Annotation and Training Cellpose\nGraphical tool for quickly creating image segmentation annotations and training custom [Cellpose](https://www.cellpose.org) models.\n\nMain features:\n1. Select regions of interests using Napari (from one or multiple images)\n2. Create cell annotations using QuPath or Napari \n3. Train a new Cellpose model (with the option to train your model via the browser using a remote server with GPU and CUDA support) or export the training data and train a new model using the `cellpose\u003e=2.0` interface.\n\nTo install it, see the [documentation](https://abailoni.github.io/cellpose-training-gui). \n\n![](docs/cellpose-training-gui/images/starting-gui-v0.2.jpg)\n\n## Features\n### Select regions of interests in Napari\nLoad one or more images (with one or multiple channels) and select the areas that you want to annotate and use for training.\n\n![](docs/cellpose-training-gui/images/selecting_rois.jpg)\n\n### Create annotations in QuPath or Napari\nGet a QuPath project that you can directly use to annotate the regions you selected, or annotate them directly using Napari. Otherwise, you can also export the regions you selected in the format expected by the cellpose software and label them in cellpose \n\n![](docs/cellpose-training-gui/images/qupath/qupath-starting-interface.jpg)\n\n### Train custom cellpose models\nTrain a new model directly from the tool, or export the training data and train a new model using the `cellpose\u003e=2.0` interface.\n\n![](docs/cellpose-training-gui/images/new_training_GUI.jpg)\n\n#### Train custom model on a remote server\nIf your machine does not have a GPU and CUDA support, you can install the `TrainCellposeServer` tool on a remote server with a GPU and train your models remotely via the browser (see [Cellpose training server tool](https://github.com/abailoni/cellpose-training-server)). \n\n![](docs/cellpose-training-gui/images/training-remotely.gif)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fabailoni%2Fcellpose-training-gui","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fabailoni%2Fcellpose-training-gui","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fabailoni%2Fcellpose-training-gui/lists"}