{"id":16346577,"url":"https://github.com/marcomusy/welsh_embryo_stager","last_synced_at":"2025-07-08T01:13:55.978Z","repository":{"id":113612006,"uuid":"469851698","full_name":"marcomusy/welsh_embryo_stager","owner":"marcomusy","description":"staging system retuned for a specific dataset","archived":false,"fork":false,"pushed_at":"2024-03-08T14:18:20.000Z","size":3401,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"main","last_synced_at":"2024-12-28T02:44:31.088Z","etag":null,"topics":[],"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/marcomusy.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":"2022-03-14T18:08:56.000Z","updated_at":"2024-07-09T03:31:15.000Z","dependencies_parsed_at":"2023-07-06T21:15:32.889Z","dependency_job_id":null,"html_url":"https://github.com/marcomusy/welsh_embryo_stager","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/marcomusy%2Fwelsh_embryo_stager","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/marcomusy%2Fwelsh_embryo_stager/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/marcomusy%2Fwelsh_embryo_stager/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/marcomusy%2Fwelsh_embryo_stager/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/marcomusy","download_url":"https://codeload.github.com/marcomusy/welsh_embryo_stager/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":239550231,"owners_count":19657541,"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":[],"created_at":"2024-10-11T00:35:41.891Z","updated_at":"2025-02-18T21:20:32.812Z","avatar_url":"https://github.com/marcomusy.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Welsh Mouse Embryo Stager\n\nStage a mouse embryo in the age range `E14` -\u003e `E15` by drawing a spline on a photographic image.\n\n## Install and run\n\n- Install miniconda (if needed) from [here](https://docs.conda.io/en/latest/miniconda.html).\n\n- Install [`vedo`](https://vedo.embl.es/) and `scipy` by typing:\n```bash\npip install vedo -U\nconda install scipy\n```\n\n- Copy the repository locally\n```bash\ngit clone https://github.com/marcomusy/welsh_embryo_stager.git\ncd welsh_embryo_stager\n```\n\n- Run the program, eg.:\n```bash\npython stager.py pics/E14.5_L3-03_HL2.5X.jpg\n```\n\n- Draw a spline by clicking points on your image\n\n![](https://user-images.githubusercontent.com/32848391/158235171-80618fb1-ae35-4a30-8279-4dabdd35a92d.png)\n\n\n- Can also read and stage a text file directly with, eg.:\n```bash\npython stager.py pics/E14.5_L3-03_HL2.5X_LHL.txt\n```\n\n5. Press `q` when finished, an output window will show up with the age of the embryo\n\n![](https://github.com/marcomusy/welsh_embryo_stager/assets/32848391/10acd68d-af42-486e-a4cf-86745801e837)\n\nThe above output image and a text file with clicked points are saved to directory `output/` for reference.\n\n### Description\n\nUse three shape descriptors to calibrate the age over a dataset of about 190 embryos.\nThe algorithm gives reliable estimates only in the range `E14` to `E15`,\n**outside of this range results are not reliable.**\nUser should check that finger peaks and valleys (marked in green and red)\non the left plot are reasonably well identified.\n\nThe error estimation is completely heuristic and should be taken as a rough indication,\nthe red sphere represents the uncertainty in the parameter space.\nYou can interact with the 3D scene of the bottom-right plot.\n\n\n### To generate a standalone executable\nWith `pyinstaller` do:\n```bash\nrm build dist __pycache__\npyinstaller stager.spec\n```\nThis will create a `dist/stager.exe` file, which you can test with e.g.:\n```bash\ndist/stager.exe pics/E14.5_L3-03_HL2.5X.jpg\n```\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmarcomusy%2Fwelsh_embryo_stager","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmarcomusy%2Fwelsh_embryo_stager","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmarcomusy%2Fwelsh_embryo_stager/lists"}