{"id":37641529,"url":"https://github.com/jkobject/hackathon_bio_ai","last_synced_at":"2026-01-16T11:18:30.632Z","repository":{"id":266815854,"uuid":"899419073","full_name":"jkobject/hackathon_bio_ai","owner":"jkobject","description":null,"archived":false,"fork":false,"pushed_at":"2024-12-23T19:30:11.000Z","size":56743,"stargazers_count":2,"open_issues_count":1,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-12-13T03:56:21.986Z","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/jkobject.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":"2024-12-06T08:22:18.000Z","updated_at":"2025-05-08T13:59:19.000Z","dependencies_parsed_at":"2024-12-06T10:35:44.171Z","dependency_job_id":null,"html_url":"https://github.com/jkobject/hackathon_bio_ai","commit_stats":null,"previous_names":["jkobject/hackaton_bio_ai"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/jkobject/hackathon_bio_ai","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jkobject%2Fhackathon_bio_ai","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jkobject%2Fhackathon_bio_ai/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jkobject%2Fhackathon_bio_ai/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jkobject%2Fhackathon_bio_ai/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/jkobject","download_url":"https://codeload.github.com/jkobject/hackathon_bio_ai/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jkobject%2Fhackathon_bio_ai/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28478200,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-16T06:30:42.265Z","status":"ssl_error","status_checked_at":"2026-01-16T06:30:16.248Z","response_time":107,"last_error":"SSL_read: 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":[],"created_at":"2026-01-16T11:18:29.792Z","updated_at":"2026-01-16T11:18:30.626Z","avatar_url":"https://github.com/jkobject.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Bio AI Hackathon 2024\n\n![image](./main.png)\n\nFunctionality:\n\n- Getting embeddings using CONCH 1.5 for patches and TITAN for slides\n- Scripts to run [scPRINT](https://github.com/mahmoodlab/HEST) on spatial xenium datasets to get cell types and full gene expression\n- Downloader / converter of HEST1K to spatial data files in Lamindb\n- DataLoader for spatialdata\n- Extract embeddings from TITAN and store in .obsm() and ask questions\n- Buttons and Textboxs to Napari to ask questions and search for patches\n\n### 1. Install the package in editable mode\n\n```bash\ngit clone git@github.com:jkobject/hackathon_bio_ai.git\ncd hackathon_bio_ai\nconda create -n st_challenge_dev python=3.10\nconda activate st_challenge_dev\npip install -e .\n```\n\n### Install the package\n\n```bash\nconda create -n st_challenge_prod python=3.10\nconda activate st_challenge_prod\npip install git+https://github.com/jkobject/hackathon_bio_ai.git\n```\n\n\n### 4. View an image\n```bash\nconda activate theremia\npython -m st_challenge.scripts.viz_slice INT1\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjkobject%2Fhackathon_bio_ai","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjkobject%2Fhackathon_bio_ai","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjkobject%2Fhackathon_bio_ai/lists"}