{"id":24366974,"url":"https://github.com/zoccoler/lifetime-unmixing","last_synced_at":"2025-04-10T13:22:43.800Z","repository":{"id":271874615,"uuid":"889236818","full_name":"zoccoler/Lifetime-Unmixing","owner":"zoccoler","description":null,"archived":false,"fork":false,"pushed_at":"2025-01-10T13:24:44.000Z","size":39096,"stargazers_count":3,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-03-24T12:08:32.259Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","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/zoccoler.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,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2024-11-15T21:57:54.000Z","updated_at":"2025-01-10T13:21:58.000Z","dependencies_parsed_at":"2025-01-10T13:27:28.917Z","dependency_job_id":"f40931b3-de7c-47af-90b6-b163ad173ffa","html_url":"https://github.com/zoccoler/Lifetime-Unmixing","commit_stats":null,"previous_names":["zoccoler/lifetime-unmixing"],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zoccoler%2FLifetime-Unmixing","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zoccoler%2FLifetime-Unmixing/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zoccoler%2FLifetime-Unmixing/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zoccoler%2FLifetime-Unmixing/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/zoccoler","download_url":"https://codeload.github.com/zoccoler/Lifetime-Unmixing/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248225664,"owners_count":21068078,"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":[],"created_at":"2025-01-19T01:11:25.246Z","updated_at":"2025-04-10T13:22:43.780Z","avatar_url":"https://github.com/zoccoler.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Lifetime Unmixing \n\nThis repository hosts code for distinguishing 2 dyes with overlapping spectra via lifetime.\nThe workflows presented here mainly rely on the [napari-flim-phasor-plotter](https://zenodo.org/records/13319544) plugin, along with some post-processing/analysis steps done using [pyclesperanto-prototype](https://zenodo.org/records/10432619), [scikit-image](https://scikit-image.org/) and [scikit-learn](https://scikit-learn.org/stable/index.html), plus file saving using [tifffile](https://pypi.org/project/tifffile/).\nImages of worm embryos are 6D (3D FLIM timelapse multichannel). Images of adult worms are 5D (3D FLIM multichannel).\n\n## Installation\n\nInstall [Miniforge](https://github.com/conda-forge/miniforge?tab=readme-ov-file#miniforge) in your computer (which contains [`mamba`](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html#)).\n\nClone this repository locally (for example using [Github Desktop](https://desktop.github.com/)).\n\nFrom a command line prompt, navigate to where you cloned this repository locally (for example by typing `cd Lifetime-Unmixing`) and create a specific conda environment by typing the following line:\n\n```bash\nmamba env create -f env.yml\n```\n\n## Usage\n\nFrom a terminal, activate the conda environment with:\n\n```bash\nmamba activate lifetime-env\n```\n\nThen open [jupyter lab](https://jupyter.org/) or your prefered IDE (for example VSCode, Pycharm, etc) and run the code of interest from the \"code\" folder. Remember to replace the data path with your local path to the images.\n\nWe recommend running this code on a powerful workstation, preferably with \u003e 48GB RAM and a GPU.\n\n## Acknowledgements\n\nWe thank the Bio-Image Analysis Technology Development team of Physics of Life at TU Dresden (BiA-PoL) for the provision of infrastructure, code development and fruitful discussions.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzoccoler%2Flifetime-unmixing","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fzoccoler%2Flifetime-unmixing","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzoccoler%2Flifetime-unmixing/lists"}