{"id":16284504,"url":"https://github.com/derthorsten/spatial","last_synced_at":"2025-04-09T00:05:39.999Z","repository":{"id":90542352,"uuid":"196556639","full_name":"DerThorsten/spatial","owner":"DerThorsten","description":"spatial genomics","archived":false,"fork":false,"pushed_at":"2019-08-01T14:17:10.000Z","size":114,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-02-14T18:49:06.761Z","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":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/DerThorsten.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":"CONTRIBUTING.rst","funding":null,"license":null,"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":"2019-07-12T10:06:14.000Z","updated_at":"2019-08-01T14:17:12.000Z","dependencies_parsed_at":null,"dependency_job_id":"21a8a4ca-6495-4f1a-abff-45cfcb8e54a3","html_url":"https://github.com/DerThorsten/spatial","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/DerThorsten%2Fspatial","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DerThorsten%2Fspatial/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DerThorsten%2Fspatial/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DerThorsten%2Fspatial/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/DerThorsten","download_url":"https://codeload.github.com/DerThorsten/spatial/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247947859,"owners_count":21023066,"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":"2024-10-10T19:19:45.987Z","updated_at":"2025-04-09T00:05:39.979Z","avatar_url":"https://github.com/DerThorsten.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"=================================================\nIntegrative analysis of single cell imaging mass citometry data of breast cancer patients\n=================================================\n\n.. image:: https://readthedocs.org/projects/spatial/badge/?version=latest\n        :target: http://spatial.readthedocs.io/en/latest/?badge=latest\n        :alt: Documentation Status               \n\n      \n.. image:: https://circleci.com/gh/DerThorsten/spatial/tree/master.svg?style=svg\n        :target: https://circleci.com/gh/DerThorsten/spatial/tree/master\n        :alt: CircleCI Status\n      \n\nCurrent features include: \n  * modern C++ 14\n  * build system with modernish CMake \n  \nRunning a first exploratory data analysis\n================\nFirst, install the dependencies with\n\n``conda env create -f spatial-dev-requirements.yml``\n\nand activate the corresponding conda environment\n\n``conda activate spatial-dev``\n\n\nCurrently, there is a problem in the DFKZ cluster which prevents Snakemake to be installed automatically from the ``.yml`` file, so in any machine you also need to run (from within the spatial-dev environment) the following:\n\n``conda install -c bioconda snakemake``\n\n\n=======\nIf this still does not work, you need to run the script manually instead that with Snakemake.\nNow, if you are in DKFZ cluster the data is already present (in ``/icgc/dkfzlsdf/analysis/B260/projects/spatial_zurich/data``) so, if you have been able to install Snakemake, you can run the exploratory data analysis simply with the command\n=======\nNow, if you are in DKFZ cluster the data is already present (in ``/icgc/dkfzlsdf/analysis/B260/projects/spatial_zurich/data``) so you can run the exploratory data analysis simply with the command\n\u003e\u003e\u003e\u003e\u003e\u003e\u003e c269ac8d28bf8a4b3417ffcbabd34b50ff875ea6\n\n\n\n=======\n``snakemake``\n\nIf you are not in the cluster you first need to update the code in ``folders.py`` by inserting the path of the root folder of the data in your machine. In the root folder the data must be organized into this directory tree:\n\n::\n\n    \u003cdata_root_folder\u003e/\n    ├── csv/\n    │   ├── Basel_PatientMetadata.csv\n    │   ├── Basel_Zuri_SingleCell.csv\n    │   ├── Basel_Zuri_StainingPanel.csv\n    │   ├── Basel_Zuri_WholeImage.csv\n    │   └── Zuri_PatientMetadata.csv\n    ├── Basel_Zuri_masks/\n    │   └── *.tiff (746 files)\n    └── ome/\n        └── *.tiff (746 files)\n        \nThe Data\n====\n\nThe data, from the B. Bodenmiller lab, is a collection of images acquired with Imaging Mass Citometry of breast cancer cells of different patients and under different conditions [1]_.\nEach ``.tiff`` file in the ``ome`` folder is uniquely paired with a ``.tiff`` mask. Each mask tells which are the cells.\n\nFAQ\n====\n\nQ: Is the data showing 2D sections of 3D bodies?\n\nA: No\n\n----\n\n.. [1] Schulz D, Zanotelli VRT, Bodenmiller B. et al. *Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry.* Cell Syst. 2018 Jan 24\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fderthorsten%2Fspatial","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fderthorsten%2Fspatial","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fderthorsten%2Fspatial/lists"}