{"id":27437391,"url":"https://github.com/aplbrain/vsvi2precomputed","last_synced_at":"2025-07-03T09:07:13.332Z","repository":{"id":285426041,"uuid":"781074403","full_name":"aplbrain/vsvi2precomputed","owner":"aplbrain","description":"Script to convert VSVI (used in VAST) image datasets to precomputed volumes","archived":false,"fork":false,"pushed_at":"2025-03-31T16:49:49.000Z","size":4950,"stargazers_count":0,"open_issues_count":3,"forks_count":0,"subscribers_count":5,"default_branch":"main","last_synced_at":"2025-04-14T20:38:03.587Z","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":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/aplbrain.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":"2024-04-02T17:43:58.000Z","updated_at":"2025-03-31T16:49:51.000Z","dependencies_parsed_at":"2025-03-31T17:47:58.013Z","dependency_job_id":"706a34ae-5c9a-40bb-8eab-03b35caefe66","html_url":"https://github.com/aplbrain/vsvi2precomputed","commit_stats":null,"previous_names":["aplbrain/vsvi2precomputed"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/aplbrain/vsvi2precomputed","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aplbrain%2Fvsvi2precomputed","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aplbrain%2Fvsvi2precomputed/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aplbrain%2Fvsvi2precomputed/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aplbrain%2Fvsvi2precomputed/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/aplbrain","download_url":"https://codeload.github.com/aplbrain/vsvi2precomputed/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aplbrain%2Fvsvi2precomputed/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263296487,"owners_count":23444493,"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":"2025-04-14T20:29:02.082Z","updated_at":"2025-07-03T09:07:13.311Z","avatar_url":"https://github.com/aplbrain.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# vsvi2precomputed\n![Logo](logo.png)\nPackage for converting VSVI (used in VAST) image datasets to precomputed volumes. Supports conversion of local and AWS S3 datasets.\n\nRequirements:\n* Python\n* AWS CLI (if using S3)\n\n## Usage\n\nConvert a cloud dataset and store in new cloud path:\n```\npip install -r requirements.txt\npython vsvi2precomputed.py -i s3://path/to/config.vsvi -o s3://path/to/output/dir/\n```\nDon't forget the trailing slash on the output dir.\n\nConvert a local dataset and upload to the cloud:\n```\npython vsvi2precomputed.py --i path/to/config.vsvi --o s3://path/to/output/dir/\n```\n\nConvert a cloud dataset and upload to the cloud:\n```\npython vsvi2precomputed.py --i s3://path/to/config.vsvi --o path/to/output/dir/\n```\n\nConvert a dataset locally:\n```\npython vsvi2precomputed.py --i path/to/config.vsvi --o path/to/output/dir/\n```\n\nOptional Arguments\n\n| Argument  | Description          | Default |\n|-----------|----------------------|---------|\n| --profile | AWS CLI profile name | default |\n\n## Tests\n```\npip install pytest\npytest\n```\nTo use an non-default AWS CLI profile:\n```\npytest --profile \u003cprofile-name\u003e\n```\n\n## About VSVI and precomputed formats\n\nVSVI format is native to the [VAST](https://lichtman.rc.fas.harvard.edu/vast/) ecosystem. Precomputed format is native to the [Neuroglancer](https://github.com/google/neuroglancer)/[CloudVolume](https://github.com/seung-lab/cloud-volume) ecosystem.\n\nTo view converted data in Neuroglancer:\n* Navigate to neuroglancer.bossdb.io.\n* Add a new layer using the Data Source URL input box on the top right. \n  * S3: The Data Source URL will be the S3 URI of the directory containing the info file, prepended with `precomputed://`. Example: `precomputed://s3://mambo-datalake/connects49a/vsvi2precomputed/local_aligned/`. \n  * Local: You will need to serve the data first. Navigate to the directory containing the info file, then open a terminal and run the following code. The Data Source URL will then follow the format `precomputed://localhost:\u003cport\u003e/`.\n  ```\n  from cloudvolume import CloudVolume\n  cv = CloudVolume(\"file://.\")\n  cv.viewer()\n  ```\n  * Click the yellow \"Create as image layer\" button at the bottom right.\n\n## Acknowledgements\n\nWe thank the Visual Computing Group at Harvard for building the VAST software. https://www.frontiersin.org/journals/neural-circuits/articles/10.3389/fncir.2018.00088/full \n\n---\nCopyright (c) 2024 The Johns Hopkins University Applied Physics Laboratory LLC.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faplbrain%2Fvsvi2precomputed","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Faplbrain%2Fvsvi2precomputed","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faplbrain%2Fvsvi2precomputed/lists"}