{"id":21318825,"url":"https://github.com/sydney-informatics-hub/tiff2vrml","last_synced_at":"2025-03-15T22:14:58.394Z","repository":{"id":205678612,"uuid":"714813730","full_name":"Sydney-Informatics-Hub/tiff2vrml","owner":"Sydney-Informatics-Hub","description":"Takes a stack of TIFF files and converts to a 3D VRML file","archived":false,"fork":false,"pushed_at":"2023-11-16T11:50:54.000Z","size":392,"stargazers_count":1,"open_issues_count":1,"forks_count":0,"subscribers_count":6,"default_branch":"main","last_synced_at":"2025-01-22T11:13:05.422Z","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/Sydney-Informatics-Hub.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}},"created_at":"2023-11-05T21:59:35.000Z","updated_at":"2023-11-05T23:02:35.000Z","dependencies_parsed_at":null,"dependency_job_id":"3dbe6fcd-601d-4ca4-b27e-1b6d3b041825","html_url":"https://github.com/Sydney-Informatics-Hub/tiff2vrml","commit_stats":null,"previous_names":["sydney-informatics-hub/tiff2vrml"],"tags_count":0,"template":false,"template_full_name":"Sydney-Informatics-Hub/imod-contained","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sydney-Informatics-Hub%2Ftiff2vrml","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sydney-Informatics-Hub%2Ftiff2vrml/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sydney-Informatics-Hub%2Ftiff2vrml/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sydney-Informatics-Hub%2Ftiff2vrml/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Sydney-Informatics-Hub","download_url":"https://codeload.github.com/Sydney-Informatics-Hub/tiff2vrml/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243796741,"owners_count":20349264,"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":"2024-11-21T19:23:53.120Z","updated_at":"2025-03-15T22:14:58.375Z","avatar_url":"https://github.com/Sydney-Informatics-Hub.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n# Helper code\n\n```\nimport numpy as np\nimport tifffile as tiff\nimport os\nimport scipy\nimport matplotlib.pyplot as plt\n\n# Read the tiff files, assume have sorteable filenames 001.tif, 002.tif etc.\ntiff_dir = \"data/\"\ntiff_files = [f for f in os.listdir(tiff_dir) if f.endswith(\".tif\")]\ntiff_files.sort()\n\n# Load the first TIFF file to get its dimensions\nfirst_tiff = tiff_files[0]\nheight, width = first_tiff.shape\nnum_slices = len(tiff_files)\n\n# Create a numpy array to store the volume\nvolume = np.zeros((height, width, num_slices), dtype=np.uint8)\n\n# Iterate through TIFF files and populate a volume\nfor i, tiff_file in enumerate(tiff_files):\n  print(tiff_file)\n  tiff_data = tiff.imread(os.path.join(tiff_dir, tiff_file))\n  volume[:, :, i] = tiff_data\n```\n\n# Try\n* Open3d\n* vtk\n* ?? others\n\n# Now do magic\nExport vrml\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsydney-informatics-hub%2Ftiff2vrml","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsydney-informatics-hub%2Ftiff2vrml","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsydney-informatics-hub%2Ftiff2vrml/lists"}