{"id":49921742,"url":"https://github.com/emcramer/tmelandscape","last_synced_at":"2026-05-29T01:00:56.129Z","repository":{"id":357526203,"uuid":"1237159170","full_name":"emcramer/tmelandscape","owner":"emcramer","description":null,"archived":false,"fork":false,"pushed_at":"2026-05-14T23:28:55.000Z","size":2583,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2026-05-16T20:48:17.000Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/emcramer.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":"AGENTS.md","dco":null,"cla":null}},"created_at":"2026-05-12T23:49:25.000Z","updated_at":"2026-05-14T23:28:41.000Z","dependencies_parsed_at":null,"dependency_job_id":null,"html_url":"https://github.com/emcramer/tmelandscape","commit_stats":null,"previous_names":["emcramer/tmelandscape"],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/emcramer/tmelandscape","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/emcramer%2Ftmelandscape","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/emcramer%2Ftmelandscape/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/emcramer%2Ftmelandscape/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/emcramer%2Ftmelandscape/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/emcramer","download_url":"https://codeload.github.com/emcramer/tmelandscape/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/emcramer%2Ftmelandscape/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":33632271,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-05-28T02:00:06.440Z","response_time":99,"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":"2026-05-16T20:37:01.103Z","updated_at":"2026-05-29T01:00:56.119Z","avatar_url":"https://github.com/emcramer.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# tmelandscape\n\n[![License: BSD-3-Clause](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](LICENSE)\n\n**tmelandscape** generates tumor microenvironment (TME) state landscapes from agent-based model (ABM) simulation ensembles. It implements the parameter sampling, spatial-statistic summarisation, time-delay embedding, and clustering steps of the trajectory-landscape pipeline described in EM. Cramer, LM. Heiser and YH. Chang, \"Trajectory Landscapes for Therapeutic Strategy Design in Agent-Based Tumor Microenvironment Models,\" in _IEEE Control Systems Letters_, [doi: 10.1109/LCSYS.2026.3697136](\u003chttps://doi.org/10.1109/LCSYS.2026.3697136\u003e).\n\n\u003e **Status:** pre-alpha (v0.0.1). API is not yet stable.\n\n## Pipeline scope\n\n`tmelandscape` implements steps **1**, **3**, **4**, and **5** below; step 2 (running ABM simulations) is handled by a separate tool.\n\n1. **Sample** ABM parameter space (Latin Hypercube via [pyDOE3](https://pypi.org/project/pyDOE3/)) and pair with initial cell positions from [`tissue_simulator`](https://github.com/emcramer/tissue_simulator). Produces a sweep manifest.\n2. *(External)* **Run** PhysiCell simulations for each manifest row. Out of scope.\n3. **Summarise** each simulation with spatial statistics via [`spatialtissuepy`](https://github.com/emcramer/spatialtissuepy); aggregate into a chunked Zarr store.\n4. **Embed** the spatial-statistic time series with time-delay (Takens) embedding; optimise dimension via False Nearest Neighbours and lag via mutual information.\n5. **Cluster** the embedding to identify discrete TME states (default: hierarchical agglomerative + Ward).\n\n## Quick start\n\n```bash\n# 1. Install uv (https://docs.astral.sh/uv/)\n# 2. Sync the environment\nuv sync --all-extras\n\n# 3. Run tests\nuv run pytest\n\n# 4. Serve the docs locally\nuv run mkdocs serve\n\n# 5. Start the MCP server (for LLM agents)\nuv run tmelandscape-mcp\n```\n\n## Documentation\n\nFull docs live at \u003chttps://emcramer.github.io/tmelandscape/\u003e (once published). Locally:\n\n```bash\nuv run mkdocs serve\n```\n\nKey documents:\n\n- [Project roadmap](docs/development/ROADMAP.md)\n- [Current status / handoff](docs/development/STATUS.md)\n- [Architecture Decision Records](docs/adr/)\n- [Agent handoff conventions](AGENTS.md)\n\n## License\n\nBSD 3-Clause. See [LICENSE](LICENSE).\n\n## Citing\n\nSee [CITATION.cff](CITATION.cff) for the software citation; cite the following manuscripts for the methodology:\n\n\u003e 1. Cramer, E., Heiser, L. M. \u0026 Chang, Y. H. Trajectory Landscapes for Therapeutic Strategy Design in Agent-Based Tumor Microenvironment Models. Preprint at https://doi.org/10.48550/arXiv.2603.18333 (2026).\n\u003e 2. Cramer, E. M. et al. Tumor-immune trajectory context connects static tissue architecture to clinical outcomes. 2026.03.26.714521 Preprint at https://doi.org/10.64898/2026.03.26.714521 (2026).\n\n \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Femcramer%2Ftmelandscape","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Femcramer%2Ftmelandscape","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Femcramer%2Ftmelandscape/lists"}