{"id":27873297,"url":"https://github.com/wpbonelli/herbarium-sheets","last_synced_at":"2025-10-07T04:24:58.783Z","repository":{"id":149700033,"uuid":"392053864","full_name":"wpbonelli/herbarium-sheets","owner":"wpbonelli","description":"trait analysis for digitized herbarium sheets","archived":false,"fork":false,"pushed_at":"2021-08-07T21:29:57.000Z","size":99,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-05-05T01:09:02.017Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","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/wpbonelli.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":"2021-08-02T18:26:32.000Z","updated_at":"2024-12-09T13:40:02.000Z","dependencies_parsed_at":"2023-09-11T18:01:10.701Z","dependency_job_id":"971481ff-1651-4e00-b3d3-033a98b1130d","html_url":"https://github.com/wpbonelli/herbarium-sheets","commit_stats":null,"previous_names":["wpbonelli/herbarium-sheets"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/wpbonelli%2Fherbarium-sheets","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/wpbonelli%2Fherbarium-sheets/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/wpbonelli%2Fherbarium-sheets/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/wpbonelli%2Fherbarium-sheets/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/wpbonelli","download_url":"https://codeload.github.com/wpbonelli/herbarium-sheets/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252420954,"owners_count":21745154,"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":"2025-05-05T01:09:04.853Z","updated_at":"2025-10-07T04:24:53.753Z","avatar_url":"https://github.com/wpbonelli.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Herbarium Sheets\n\nExtract geometric trait measurements from scans or images of herbarium sheets.\n\n## Acknowledgements\n\nGeneral approach inspired by Suxing Liu, in particular [Smart Plant Growth Top-Down Traits](https://github.com/Computational-Plant-Science/spg).\n\n[PlantCV](https://github.com/danforthcenter/plantcv) also used for skeletonization, pruning, leaf \u0026 stem counting, etc.\n\n## Requirements\n\n[Docker](https://www.docker.com/) is required to run this project in a Unix environment.\n\n## Installation\n\nTo install from source, clone the project with `git clone https://github.com/w-bonelli/herbarium-sheets.git`, then build the image from the root directory with `docker build -t \u003cyour tag\u003e -f Dockerfile .`.\n\nAlternatively, you can just pull the pre-built image with `docker pull wbonelli/herbarium-sheets`, or allow it to be pulled automatically from another Docker CLI command (as below).\n\n## Usage\n\nTo analyze an image:\n\n```bash\ndocker run wbonelli/herbarium-sheets python3.8 /opt/code/cli.py \u003cinput file\u003e\n```\n\nBy default, output files will be written to the current working directory. To specify a different output location, use `-o \u003cfull path to output directory\u003e`.\n\n## Development\n\nTo set up a development environment and explore or modify the source, just mount the project root as your container's working directory, for instance:\n\n```bash\ndocker run -it -v $(pwd):/opt/dev -w /opt/dev wbonelli/herbarium-sheets bash\n```\n\nThen invoke the CLI with `python3.8 /opt/code/cli.py \u003cinput file\u003e`.\n\nGit is also instructed to ignore `data` and `output` directories for convenience.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fwpbonelli%2Fherbarium-sheets","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fwpbonelli%2Fherbarium-sheets","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fwpbonelli%2Fherbarium-sheets/lists"}