{"id":13716708,"url":"https://github.com/fish-quant/big-fish","last_synced_at":"2025-05-07T06:30:53.657Z","repository":{"id":40721394,"uuid":"162127052","full_name":"fish-quant/big-fish","owner":"fish-quant","description":"Toolbox for the analysis of smFISH images.","archived":false,"fork":false,"pushed_at":"2023-10-31T13:49:32.000Z","size":13530,"stargazers_count":56,"open_issues_count":16,"forks_count":18,"subscribers_count":8,"default_branch":"master","last_synced_at":"2024-11-05T03:37:33.835Z","etag":null,"topics":["pattern-classification","rna-localization","segmentation","smfish","spatial-features","spot-detection"],"latest_commit_sha":null,"homepage":"https://big-fish.readthedocs.io/en/stable/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/fish-quant.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}},"created_at":"2018-12-17T12:26:09.000Z","updated_at":"2024-10-18T14:43:28.000Z","dependencies_parsed_at":"2022-07-29T05:48:10.772Z","dependency_job_id":"34aac8da-cd91-4c3e-b6cd-544535ed632c","html_url":"https://github.com/fish-quant/big-fish","commit_stats":{"total_commits":553,"total_committers":4,"mean_commits":138.25,"dds":0.007233273056057921,"last_synced_commit":"e951ea850b18be4be70c5d0a419ba524c3a59ada"},"previous_names":[],"tags_count":8,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fish-quant%2Fbig-fish","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fish-quant%2Fbig-fish/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fish-quant%2Fbig-fish/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fish-quant%2Fbig-fish/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/fish-quant","download_url":"https://codeload.github.com/fish-quant/big-fish/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224567731,"owners_count":17332830,"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":["pattern-classification","rna-localization","segmentation","smfish","spatial-features","spot-detection"],"created_at":"2024-08-03T00:01:13.551Z","updated_at":"2024-11-14T04:32:08.899Z","avatar_url":"https://github.com/fish-quant.png","language":"Python","funding_links":[],"categories":["🔍 Object detection","Fluoresence in situ hybridization"],"sub_categories":["Spots"],"readme":"# Big-FISH\n\n[![PyPI version](https://badge.fury.io/py/big-fish.svg)](https://badge.fury.io/py/big-fish)\n[![Build Status](https://travis-ci.com/fish-quant/big-fish.svg?branch=master)](https://travis-ci.com/fish-quant/big-fish)\n[![Documentation Status](https://readthedocs.org/projects/big-fish/badge/?version=stable)](https://big-fish.readthedocs.io/en/latest/?badge=stable)\n[![codecov](https://codecov.io/gh/fish-quant/big-fish/branch/master/graph/badge.svg)](https://codecov.io/gh/fish-quant/big-fish)\n[![License](https://img.shields.io/badge/license-BSD%203--Clause-green)](https://github.com/fish-quant/big-fish/blob/master/LICENSE)\n[![Python version](https://img.shields.io/pypi/pyversions/big-fish.svg)](https://pypi.python.org/pypi/big-fish/)\n\n**Big-FISH** is a python package for the analysis of smFISH images. It includes various methods to **analyze microscopy images**, such **spot detection** and **segmentation of cells and nuclei**. The package allows the user represent the extract properties of a cell as coordinates (see figure below). The ultimate goal is to simplify **large scale statistical analysis** and quantification.\n\n| Cell image (smFISH channel) and its coordinates representation |\n| ------------- |\n| ![](images/plot_cell.png \"Nucleus in blue, mRNAs in red, foci in orange and transcription sites in green\") |\n\n## Installation\n\n### Dependencies\n\nBig-FISH requires Python 3.6 or newer. Additionally, it has the following dependencies:\n\n- numpy (\u003e= 1.16.0)\n- scipy (\u003e= 1.4.1)\n- scikit-learn (\u003e= 0.24.0)\n- scikit-image (\u003e= 0.14.2)\n- matplotlib (\u003e= 3.0.2)\n- pandas (\u003e= 0.24.0)\n- mrc (\u003e= 0.1.5)\n\nFor segmentation purpose, two additional dependencies can be requested:\n- tensorflow (== 2.3.0)\n- tensorflow-addons (== 0.12.1)\n\n### Virtual environment\n\nTo avoid dependency conflicts, we recommend the the use of a dedicated [virtual](https://docs.python.org/3.6/library/venv.html) or [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) environment.  In a terminal run the command:\n\n```bash\nconda create -n bigfish_env python=3.6\nsource activate bigfish_env\n```\n\nWe recommend two options to then install Big-FISH in your virtual environment.\n\n#### Download the package from PyPi\n\nUse the package manager [pip](https://pip.pypa.io/en/stable/) to install Big-FISH. In a terminal run the command:\n\n```bash\npip install big-fish\n```\n\n#### Clone package from Github\n\nClone the project's [Github repository](https://github.com/fish-quant/big-fish) and install it manually with the following commands:\n\n```bash\ngit clone git@github.com:fish-quant/big-fish.git\ncd big-fish\npip install .\n```\n\n## Usage\n\nBig-FISH provides a toolbox for the full analysis pipeline of smFISH images. A complete [documentation](https://big-fish.readthedocs.io/en/stable/) is available online. \n\nThis package is part of the [FISH-Quant](https://fish-quant.github.io/) framework and several examples are also available as [Jupyter notebooks](https://github.com/fish-quant/big-fish-examples/tree/master/notebooks).\n\n## Support\n\nIf you have any question relative to the repository, please open an [issue](https://github.com/fish-quant/big-fish/issues). You can also contact [Arthur Imbert](mailto:arthur.imbert@mines-paristech.fr) or [Florian Mueller](mailto:muellerf.research@gmail.com).\n\n## Roadmap (suggestion)\n\nVersion 1.0.0:\n- Complete code coverage.\n- Unpin deep learning dependencies\n- Add a pretrained pattern recognition model\n\n## Development\n\n### Source code\n\nYou can access the latest sources with the commands:\n\n```bash\ngit clone git@github.com:fish-quant/big-fish.git\ncd big-fish\ngit checkout develop\n```\n\n### Contributing\n\n[Pull requests](https://github.com/fish-quant/big-fish/pulls) are welcome. For major changes, please open an [issue](https://github.com/fish-quant/big-fish/issues) first to discuss what you would like to change.\n\n### Testing\n\nPlease make sure to update tests as appropriate if you open a pull request. You can install exacts dependencies and specific version of [pytest](https://docs.pytest.org/en/latest/) by running the following command:\n\n```bash\npip install -r requirements_dev.txt\n```\n\nTo perform unit tests, run : \n\n```bash\npytest bigfish\n```\n\n## Citation\n\nIf you exploit this package for your work, please cite:\n\n\u003e Arthur Imbert, Wei Ouyang, Adham Safieddine, Emeline Coleno, Christophe Zimmer, Edouard Bertrand, Thomas Walter, Florian Mueller. FISH-quant v2: a scalable and modular analysis tool for smFISH image analysis. bioRxiv (2021) https://doi.org/10.1101/2021.07.20.453024\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffish-quant%2Fbig-fish","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffish-quant%2Fbig-fish","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffish-quant%2Fbig-fish/lists"}