{"id":16506219,"url":"https://github.com/keller-mark/visium-dlpfc-processing","last_synced_at":"2026-06-06T18:32:09.498Z","repository":{"id":225403809,"uuid":"765336009","full_name":"keller-mark/visium-dlpfc-processing","owner":"keller-mark","description":null,"archived":false,"fork":false,"pushed_at":"2024-03-04T18:07:33.000Z","size":440,"stargazers_count":1,"open_issues_count":1,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-01-12T14:13:50.964Z","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":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/keller-mark.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"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}},"created_at":"2024-02-29T18:12:52.000Z","updated_at":"2024-03-01T23:28:40.000Z","dependencies_parsed_at":"2024-03-01T22:43:55.470Z","dependency_job_id":null,"html_url":"https://github.com/keller-mark/visium-dlpfc-processing","commit_stats":null,"previous_names":["keller-mark/visium-dlpfc-processing"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/keller-mark%2Fvisium-dlpfc-processing","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/keller-mark%2Fvisium-dlpfc-processing/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/keller-mark%2Fvisium-dlpfc-processing/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/keller-mark%2Fvisium-dlpfc-processing/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/keller-mark","download_url":"https://codeload.github.com/keller-mark/visium-dlpfc-processing/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241444265,"owners_count":19963777,"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":"2024-10-11T15:17:58.471Z","updated_at":"2026-06-06T18:32:09.433Z","avatar_url":"https://github.com/keller-mark.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# visium-dlpfc\n\nSample 151673\n\nData obtained from:\n- RData file: https://www.dropbox.com/s/f4wcvtdq428y73p/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata?dl=1 (linked from https://github.com/LieberInstitute/spatialLIBD/blob/ff49a2eaa1eb5477c5df8e46cf1652cdd8ec7244/R/fetch_data.R#L142C18-L142C125)\n- Manual layer annotations: https://drive.google.com/drive/folders/10lhz5VY7YfvHrtV40MwaqLmWz56U9eBP?usp=sharing (linked from https://stagate.readthedocs.io/en/latest/T1_DLPFC.html)\n- TIFF image: https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151673_full_image.tif (linked from https://github.com/LieberInstitute/spatialLIBD/blob/ff49a2eaa1eb5477c5df8e46cf1652cdd8ec7244/README.md?plain=1#L235)\n\nData conversion\n\n## RData to rds\n\n```R\nload(\"Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata\")\nsaveRDS(sce, file=\"Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.rds\")\n```\n\n## rds to AnnData with manual layer annotations\n\nSee Jupyter notebook `convert_rds_to_adata.ipynb`\n\n## All to SpatialData\n\nSee Jupyter notebook `convert_all_to_spatialdata.ipynb`\n\n\n## To obtain scale factors\n\n```R\n\u003e library(STexampleData)\n\u003e spe \u003c- Visium_humanDLPFC()\n\u003e imgData(spe)\nDataFrame with 2 rows and 4 columns\n      sample_id    image_id   data scaleFactor\n    \u003ccharacter\u003e \u003ccharacter\u003e \u003clist\u003e   \u003cnumeric\u003e\n1 sample_151673      lowres   ####   0.0450045\n2 sample_151673       hires   ####   0.1500150\n\n\u003e imgData(spe)[1, 'data']\n[[1]]\n600 x 600 (width x height) LoadedSpatialImage\n\n\u003e imgData(spe)[2, 'data']\n[[1]]\n2000 x 2000 (width x height) LoadedSpatialImage\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkeller-mark%2Fvisium-dlpfc-processing","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkeller-mark%2Fvisium-dlpfc-processing","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkeller-mark%2Fvisium-dlpfc-processing/lists"}