{"id":17027103,"url":"https://github.com/lucasrla/wsi-preprocessing-sos-workflow","last_synced_at":"2026-01-04T19:06:40.913Z","repository":{"id":85923395,"uuid":"292694414","full_name":"lucasrla/wsi-preprocessing-sos-workflow","owner":"lucasrla","description":"A pipeline to preprocess whole-slide images (WSI) towards deep learning","archived":false,"fork":false,"pushed_at":"2020-09-04T22:50:51.000Z","size":15,"stargazers_count":4,"open_issues_count":0,"forks_count":2,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-03-21T00:12:06.576Z","etag":null,"topics":["deep-learning","histopathology","pathology","preprocessing","sos","sos-workflow","whole-slide-imaging"],"latest_commit_sha":null,"homepage":"","language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/lucasrla.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"COPYING","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":"2020-09-03T22:37:30.000Z","updated_at":"2023-05-24T19:15:19.000Z","dependencies_parsed_at":null,"dependency_job_id":"5cec6608-d56e-4150-b29d-e7bef8c88792","html_url":"https://github.com/lucasrla/wsi-preprocessing-sos-workflow","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/lucasrla%2Fwsi-preprocessing-sos-workflow","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lucasrla%2Fwsi-preprocessing-sos-workflow/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lucasrla%2Fwsi-preprocessing-sos-workflow/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lucasrla%2Fwsi-preprocessing-sos-workflow/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lucasrla","download_url":"https://codeload.github.com/lucasrla/wsi-preprocessing-sos-workflow/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245009608,"owners_count":20546541,"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":["deep-learning","histopathology","pathology","preprocessing","sos","sos-workflow","whole-slide-imaging"],"created_at":"2024-10-14T07:46:05.480Z","updated_at":"2026-01-04T19:06:35.890Z","avatar_url":"https://github.com/lucasrla.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# wsi-preprocessing-sos-workflow\n\nA simple pipeline built with [SoS Workflow](https://vatlab.github.io/sos-docs/workflow.html) that runs [wsi-preprocessing](https://github.com/lucasrla/wsi-preprocessing) on a remote machine.\n\n[wsi-preprocessing](https://github.com/lucasrla/wsi-preprocessing) is a simple library for preprocessing histopathological whole-slide images (WSI) towards deep learning. Check out its [repository](https://github.com/lucasrla/wsi-preprocessing).\n\nIf you do not have a remote machine ready, you can launch a new AWS EC2 instance with [ec2-setup-sos-workflow](https://github.com/lucasrla/ec2-setup-sos-workflow).\n\n\n## Installation\n\n### conda\n\n```sh\nconda create --name YOUR_ENV_NAME --channel conda-forge python=3.6 pyyaml boto3 sos black\n# black is optional, it is sort of a development dependency\n\ngit clone https://github.com/lucasrla/wsi-preprocessing-sos-workflow\n\ncd wsi-preprocessing-sos-workflow\n\nconda activate YOUR_ENV_NAME\n```\n\n### poetry or pip\n\n```sh\ngit clone https://github.com/lucasrla/wsi-preprocessing-sos-workflow\n\ncd wsi-preprocessing-sos-workflow\n\n# create and activate a virtualenv, for example:\npyenv virtualenv YOUR_ENV_NAME \u0026\u0026 pyenv local YOUR_ENV_NAME\n\n# install the dependencies, either with:\npoetry install\n# or:\npip install -r requirements.txt\n\n# note, requirements.txt in this repository were generated via:\n# poetry export --without-hashes -f requirements.txt -o requirements.txt\n```\n\n\n## Configuration\n\n```sh\n# edit project.TEMPLATE.yml to match your needs\nvim project.TEMPLATE.yml\n# and then save it as project.yml\n\n# make sure that ~/.sos/hosts.yml has the path to your pem_file \n# and that the naming of hosts matches project.yml\nvim ~/.sos/hosts.yml\n```\n\n\n## Usage\n\n```sh\nsos run -c project.yml remote.sos -v4\n```\n\nFor more tips and tricks on SoS, read the [official docs](https://vatlab.github.io/sos-docs/workflow.html). \n\nYou can also have a look at [ec2-setup-sos-workflow](https://github.com/lucasrla/ec2-setup-sos-workflow).\n\n\n## License\n\nThis is [Free Software](https://www.gnu.org/philosophy/free-sw.html) distributed under the [GNU General Public License v3.0](https://choosealicense.com/licenses/gpl-3.0/).","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flucasrla%2Fwsi-preprocessing-sos-workflow","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flucasrla%2Fwsi-preprocessing-sos-workflow","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flucasrla%2Fwsi-preprocessing-sos-workflow/lists"}