{"id":13708741,"url":"https://github.com/sebastianffx/stainlib","last_synced_at":"2025-05-06T15:31:10.023Z","repository":{"id":49791605,"uuid":"313639183","full_name":"sebastianffx/stainlib","owner":"sebastianffx","description":"Python 3 library for the augmentation \u0026 normalization of H\u0026E images","archived":false,"fork":false,"pushed_at":"2022-09-12T14:58:42.000Z","size":10396,"stargazers_count":51,"open_issues_count":3,"forks_count":8,"subscribers_count":3,"default_branch":"main","last_synced_at":"2024-10-22T09:49:19.918Z","etag":null,"topics":["computational-pathology","histopathology","image-augmentation","image-normalization","image-processing","pathology"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sebastianffx.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}},"created_at":"2020-11-17T14:08:14.000Z","updated_at":"2024-10-18T18:20:59.000Z","dependencies_parsed_at":"2023-01-18T05:00:56.858Z","dependency_job_id":null,"html_url":"https://github.com/sebastianffx/stainlib","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/sebastianffx%2Fstainlib","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sebastianffx%2Fstainlib/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sebastianffx%2Fstainlib/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sebastianffx%2Fstainlib/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sebastianffx","download_url":"https://codeload.github.com/sebastianffx/stainlib/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224513097,"owners_count":17323745,"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":["computational-pathology","histopathology","image-augmentation","image-normalization","image-processing","pathology"],"created_at":"2024-08-02T23:00:31.844Z","updated_at":"2024-11-13T19:30:19.907Z","avatar_url":"https://github.com/sebastianffx.png","language":"Jupyter Notebook","funding_links":[],"categories":["Software"],"sub_categories":["Model"],"readme":"# stainlib\n![Currently implemented methods in stainlib](https://drive.google.com/uc?id=1By4Nw3X0sgwxamF0qN3TqiL-B1q2qZqQ)\nThe objective with this repository is to provide an easy to use python 3 library that includes \nthe most commonly used methods for color augmentation and normalisation of histopathology images, having as input local image regions stained with H\u0026amp;E.\n\n## Pre-requisites and Installation\nThe library was developed and tested in a python 3.8 conda environment.  The following packages are required:\n- scikit-image\n- scipy\n- pillow\n- opencv-python\n- spams\n\nYou can find a complete list of the packages installed when developed the library under utils/enviroment.yml\n \nFor installing the library you can do it with pip:\npip install -e stainlib/ \n \n## Examples\nYou can find examples for using stainlib in the jupyter notebooks stainlib_augmentation.ipynb and stainlib_normalization.ipynb\n# Research\nIf this repository has helped you in your research we would value to be acknowledged in your publication.\n\n# Acknowledgement\nThis project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825292. This project is better known as the ExaMode project. The objectives of the ExaMode project are:\n1. Weakly-supervised knowledge discovery for exascale medical data.  \n2. Develop extreme scale analytic tools for heterogeneous exascale multimodal and multimedia data.  \n3. Healthcare \u0026 industry decision-making adoption of extreme-scale analysis and prediction tools.\n\nFor more information on the ExaMode project, please visit www.examode.eu. \n\n![enter image description here](https://www.examode.eu/wp-content/uploads/2018/11/horizon.jpg)  ![enter image description here](https://www.examode.eu/wp-content/uploads/2018/11/flag_yellow.png) \u003cimg src=\"https://www.examode.eu/wp-content/uploads/2018/11/cropped-ExaModeLogo_blacklines_TranspBackGround1.png\" width=\"80\"\u003e\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsebastianffx%2Fstainlib","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsebastianffx%2Fstainlib","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsebastianffx%2Fstainlib/lists"}