{"id":31065799,"url":"https://github.com/henriqueslab/rescale4dl","last_synced_at":"2025-09-15T16:57:29.701Z","repository":{"id":289642378,"uuid":"706600088","full_name":"HenriquesLab/ReScale4DL","owner":"HenriquesLab","description":"ReScale4DL: Balancing Pixel and Contextual Information for Enhanced Bioimage Segmentation","archived":false,"fork":false,"pushed_at":"2025-04-24T09:23:01.000Z","size":17389,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-04-24T10:28:11.124Z","etag":null,"topics":[],"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/HenriquesLab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.txt","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,"zenodo":null}},"created_at":"2023-10-18T09:09:57.000Z","updated_at":"2025-04-24T09:23:05.000Z","dependencies_parsed_at":"2025-04-24T10:38:20.002Z","dependency_job_id":null,"html_url":"https://github.com/HenriquesLab/ReScale4DL","commit_stats":null,"previous_names":["henriqueslab/rescale4dl"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/HenriquesLab/ReScale4DL","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HenriquesLab%2FReScale4DL","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HenriquesLab%2FReScale4DL/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HenriquesLab%2FReScale4DL/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HenriquesLab%2FReScale4DL/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/HenriquesLab","download_url":"https://codeload.github.com/HenriquesLab/ReScale4DL/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HenriquesLab%2FReScale4DL/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":275289703,"owners_count":25438494,"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","status":"online","status_checked_at":"2025-09-15T02:00:09.272Z","response_time":75,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":"2025-09-15T16:57:27.826Z","updated_at":"2025-09-15T16:57:29.694Z","avatar_url":"https://github.com/HenriquesLab.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# ReScale4DL: Balancing Pixel and Contextual Information for Enhanced Bioimage Segmentation\n\n\u003cimg src=\"https://raw.githubusercontent.com/HenriquesLab/ReScale4DL/refs/heads/main/.github/logo.png\" align=\"right\" width=\"200\"/\u003e\n\n[![Python 3.8+](https://img.shields.io/badge/python-3.12-blue.svg)](https://www.python.org/downloads/)\n[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n\nA systematic approach for determining optimal image resolution in deep learning-based microscopy segmentation, balancing accuracy with acquisition/storage costs. Following this approach, researchers can improve the sustainability and cost-effectiveness of bioimaging studies by reducing data and computing\nneeds while optimising microscopy techniques.\n\n## Key Features\n- **Resolution simulation**: Rescale images and their respective annotations (upsample and downsample)\n- **Segmentation evaluation**: Compare performance across resolutions using:\n  - Mean Intersection-over-Union (IoU)\n  - Morphological features\n  - Potential throughput\n  - Personalised metrics\n- **Visualization tools**: Generate comparative plots and sample outputs\n\n## Installation\n\nReScale4DL is available as a Python package through pip. \nActivate your conda environment or create one:\n```terminal\nconda create -n rescale4dl \"python\u003c=3.12\"\nconda activate rescale4dl\n```\n\nInstall ReScale4DL with `pip`:\n\n```terminal\npip install rescale4dl\n```\n\n### Manual installation\nManual installation using the GitHub repository\n```terminal\ngit clone https://github.com/HenriquesLab/ReScale4DL.git\ncd rescale4dl\nconda create -n rescale4dl \"python\u003c=3.12\"\nconda activate rescale4dl\npython -m pip install .\n```\n\n\n## Usage\n\n### 1. Image Rescaling\nNotebook: [`Rescale_Images.ipynb`](https://github.com/HenriquesLab/ReScale4DL/blob/main/Notebooks/Rescale_Images.ipynb)\n\n### 2. Segmentation Analysis \nNotebook: [`Evaluate_Segmentation.ipynb`](https://github.com/HenriquesLab/ReScale4DL/blob/main/Notebooks/Evaluate_Segmentation.ipynb)\n\n### 3. Rescale and crop \nNotebook: [`Rescale_Foundation_Models.ipynb`](https://github.com/HenriquesLab/ReScale4DL/blob/main/Notebooks/Rescale_Foundation_Models.ipynb)\n\n\n## Contributing\nWe welcome contributions through:\n- [Issue reporting](https://github.com/HenriquesLab/ReScale4D/issues)\n- [Pull requests](https://github.com/HenriquesLab/ReScale4D/pulls)\n\n## License\nMIT License - See [LICENSE](LICENSE) for details\n\n## How to cite this work\n\nFerreira, M.G., Saraiva, B.M., Brito, A.D., Pinho, M.G., Henriques, R. and Gómez-de-Mariscal, E., *ReScale4DL: Balancing Pixel and Contextual Information for Enhanced Bioimage Segmentation.* bioRxiv, pp.2025-04, (2025) [https://doi.org/10.1101/2025.04.09.647871](https://doi.org/10.1101/2025.04.09.647871)\n\n[![ReScale4DL-preprint](https://raw.githubusercontent.com/HenriquesLab/ReScale4DL/refs/heads/main/.github/rescale4dl-biorxiv.png)](https://www.biorxiv.org/content/10.1101/2025.04.09.647871v1)\n\n```\n@article{ferreira2025rescale4dl,\n  title={ReScale4DL: Balancing Pixel and Contextual Information for Enhanced Bioimage Segmentation},\n  author={Ferreira, Mariana G and Saraiva, Bruno M and Brito, Ant{\\'o}nio D and Pinho, Mariana G and Henriques, Ricardo and G{\\'o}mez-de-Mariscal, Estibaliz},\n  journal={bioRxiv},\n  pages={2025--04},\n  year={2025},\n  publisher={Cold Spring Harbor Laboratory},\n  URL = https://doi.org/10.1101/2025.04.09.647871\n}\n```\n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhenriqueslab%2Frescale4dl","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhenriqueslab%2Frescale4dl","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhenriqueslab%2Frescale4dl/lists"}