{"id":16141605,"url":"https://github.com/alphonsg/bimana","last_synced_at":"2025-10-25T14:10:28.499Z","repository":{"id":63905657,"uuid":"545300976","full_name":"AlphonsG/BIMANA","owner":"AlphonsG","description":"Package for performing automated bio-image analysis tasks.","archived":false,"fork":false,"pushed_at":"2023-10-16T07:59:20.000Z","size":25323,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-02-13T00:42:13.634Z","etag":null,"topics":["bioimage-analysis","bioinformatics","data-analysis","deep-learning","edge-detection","image-analysis","image-processing"],"latest_commit_sha":null,"homepage":"","language":"Python","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/AlphonsG.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2022-10-04T05:57:00.000Z","updated_at":"2023-03-07T04:37:04.000Z","dependencies_parsed_at":"2023-02-10T20:15:41.366Z","dependency_job_id":"50504a24-a19d-4401-88a1-fd365bc6edcc","html_url":"https://github.com/AlphonsG/BIMANA","commit_stats":{"total_commits":29,"total_committers":2,"mean_commits":14.5,"dds":0.2068965517241379,"last_synced_commit":"0f6dddae81202af4f15885aaeae04626556161f1"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AlphonsG%2FBIMANA","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AlphonsG%2FBIMANA/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AlphonsG%2FBIMANA/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AlphonsG%2FBIMANA/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/AlphonsG","download_url":"https://codeload.github.com/AlphonsG/BIMANA/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247535175,"owners_count":20954571,"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":["bioimage-analysis","bioinformatics","data-analysis","deep-learning","edge-detection","image-analysis","image-processing"],"created_at":"2024-10-09T23:56:09.571Z","updated_at":"2025-10-25T14:10:23.468Z","avatar_url":"https://github.com/AlphonsG.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Bimana\n\n[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)\n[![Python package](https://github.com/AlphonsG/BIMANA/actions/workflows/python-package.yaml/badge.svg?branch=dev)](https://github.com/AlphonsG/BIMANA/actions/workflows/python-package.yaml)\n[![Coverage\nStatus](https://coveralls.io/repos/github/AlphonsG/BIMANA/badge.svg?branch=dev)](https://coveralls.io/github/AlphonsG/BIMANA?branch=dev)\n[![CodeFactor](https://www.codefactor.io/repository/github/alphonsg/bimana/badge/dev)](https://www.codefactor.io/repository/github/alphonsg/bimana/overview/dev)\n[![GitHub license](https://img.shields.io/github/license/AlphonsG/BIMANA)](https://github.com/AlphonsG/BIMANA/blob/main/LICENSE)\n\n![](misc/images/bimana.png?raw=true \"Bimana Image Analysis\")\n\nPackage for performing automated bio-image analysis tasks.\n\n# Table of contents\n1. \u003ca href=\"#installation\"\u003eInstallation\u003c/a\u003e\n2. \u003ca href=\"#usage\"\u003eUsage\u003c/a\u003e\n3. \u003ca href=\"#license\"\u003eLicense\u003c/a\u003e\n4. \u003ca href=\"#community-guidelines\"\u003eCommunity Guidelines\u003c/a\u003e\n5. \u003ca href=\"#acknowledgements\"\u003eAcknowledgements\u003c/a\u003e\n## Installation \u003ca id=\"installation\"\u003e\u003c/a\u003e\n\nBimana can be installed on Linux, Windows (with 64 bit Python) \u0026 macOS and\nsupports Python 3.10 and above. It is recommended to install and run Bimana\nwithin a [virtual environment](https://docs.python.org/3/tutorial/venv.html).\n\n1. Download and install [Python](https://www.python.org/downloads/) (Bimana was\n   tested using [Python version\n   3.10.6](https://www.python.org/downloads/release/python-3106/)),\n   [Git](https://git-scm.com/) and [Git LFS](https://git-lfs.github.com/).\n   Linux and macOS users must also install [libvips](https://www.libvips.org/install.html).\n\n2. Launch the terminal (*Linux* and *macOS* users) or command prompt (*Windows* users). The proceeding commands will be entered into the opened window\u003csup\u003e1\u003c/sup\u003e.\n\n3. Create and activate a virtual environment called 'bimana-env' in your desired directory:\n\n   ```pip install --upgrade pip```\n\n   ```python -m venv bimana-env```\n\n   ```. bimana-env/bin/activate``` (*Linux* and *macOS* users) or ```bimana-env\\Scripts\\activate.bat``` (*Windows* users)\n\n4. Install PyTorch by specifying your system configuration using the official [PyTorch get started tool](https://pytorch.org/get-started/locally/) and running the generated command:\n   \u003cp style=\"text-align:center;\"\u003e\n    \u003cimg src=\"misc/images/pytorch_get_started.png\" width=\"750\" alt=\"centered image\" /\u003e\n    \u003c/p\u003e\n   For example, according to the image above, Windows users without a GPU (i.e. CPU only) will run:\n\n   ```pip3 install torch torchvision torchaudio```\n\n\n5. Clone this repository into your desired directory:\n\n   ```\n   git lfs install\n   git clone https://github.com/AlphonsG/BIMANA.git\n   ```\n\n6. Navigate into the cloned directory:\n\n    ```cd BIMANA```\n\n7. Install Bimana:\n\n   ```\n   git submodule update --init --recursive\n   pip install -e .\n   ```\n\nNotes:\n  - \u003csup\u003e1\u003c/sup\u003eConfirm that the correct python version for Bimana has been installed using the `python -V` command in the terminal. If this command does not report the correct python version, try using the `python3 -v` command instead. If the second command produces the expected result, replace all `python` and `pip` commands in this guide with `python3` and `pip3`, respectively.\n\n  - The virtual environment can be deactivated using:\n\n      ```deactivate```\n\n## Usage \u003ca id=\"usage\"\u003e\u003c/a\u003e\n\nEnter `bimana -h` or `bimana --help` within the `bimana-env` environment after installation for details on how to use Bimana.\n\nExample commands that can be used to test Bimana using input data provided in\neach folder [here](misc/examples) are given below. After\nprocessing is finished for a given folder containing input images, multiple subfolders\ncontaining generated outputs (e.g. images,  CSV files, etc) are created. Examples of these are also provided.\n\nExample commands (first run `cd misc` from the cloned repository folder):\n\n- Histological Section Analysis\n   ```\n   bimana histological-section-analysis ./examples/histological_section --staining-amount-in-tissue-area  --cilia-amount-above-tissue-area\n   ```\n\n- Tight junction analysis\n   ```\n   bimana tight-junction-analysis ./examples/tight_junctions  --analyse-tight-junctions --analyse-cells\n   ```\n   \n- Live cell imaging metrics analysis\n   ```\n   bimana live-cell-imaging metrics-file-processing ./examples/live_cell_imaging\n   ```\n\n## License \u003ca id=\"license\"\u003e\u003c/a\u003e\n\n[MIT License](LICENSE)\n\n\n## Community guidelines \u003ca id=\"community-guidelines\"\u003e\u003c/a\u003e\n\n Guidelines for third-parties wishing to:\n\n- Contribute to the software\n- Report issues or problems with the software\n- Seek support\n\ncan be found [here](CONTRIBUTING.md).\n\n## Acknowledgements \u003ca id=\"acknowledgements\"\u003e\u003c/a\u003e\n\n- https://github.com/xavysp/DexiNed\n- https://github.com/DevonsMo/IJOQ\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falphonsg%2Fbimana","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Falphonsg%2Fbimana","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falphonsg%2Fbimana/lists"}