{"id":13717240,"url":"https://github.com/Open-Science-Tools/nd2reader","last_synced_at":"2025-05-07T07:30:36.822Z","repository":{"id":41431948,"uuid":"81961382","full_name":"Open-Science-Tools/nd2reader","owner":"Open-Science-Tools","description":"Pure Python library for reading NIS Elements ND2 images and metadata","archived":false,"fork":false,"pushed_at":"2025-01-15T10:15:32.000Z","size":28440,"stargazers_count":47,"open_issues_count":29,"forks_count":30,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-04-17T13:06:57.046Z","etag":null,"topics":["microscopy","microscopy-images","nd2","nikon","nis-elements","pims"],"latest_commit_sha":null,"homepage":"https://open-science-tools.github.io/nd2reader/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Open-Science-Tools.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"COPYING","code_of_conduct":"CODE_OF_CONDUCT.md","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":"2017-02-14T15:47:40.000Z","updated_at":"2025-04-03T22:37:55.000Z","dependencies_parsed_at":"2022-09-26T17:30:17.511Z","dependency_job_id":"da3b5174-9b76-4e76-9d3c-0967e48c371a","html_url":"https://github.com/Open-Science-Tools/nd2reader","commit_stats":{"total_commits":438,"total_committers":12,"mean_commits":36.5,"dds":0.497716894977169,"last_synced_commit":"4956ec892e394e6f2c95a0b23f3d20d3a1e8277c"},"previous_names":["rbnvrw/nd2reader"],"tags_count":26,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Open-Science-Tools%2Fnd2reader","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Open-Science-Tools%2Fnd2reader/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Open-Science-Tools%2Fnd2reader/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Open-Science-Tools%2Fnd2reader/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Open-Science-Tools","download_url":"https://codeload.github.com/Open-Science-Tools/nd2reader/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252833406,"owners_count":21811177,"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":["microscopy","microscopy-images","nd2","nikon","nis-elements","pims"],"created_at":"2024-08-03T00:01:19.721Z","updated_at":"2025-05-07T07:30:36.813Z","avatar_url":"https://github.com/Open-Science-Tools.png","language":"Python","funding_links":[],"categories":["Other"],"sub_categories":[],"readme":"# nd2reader\n\n**This package is no longer actively developed because I'm no longer working in this field and can't properly maintain it. If you'd like to help, please see the [contributing](https://github.com/rbnvrw/nd2reader/blob/master/CONTRIBUTING.md) page\nfor more information.**\n\n[![Anaconda-Server Badge](https://anaconda.org/conda-forge/nd2reader/badges/version.svg)](https://anaconda.org/conda-forge/nd2reader)\n[![Anaconda-Server Badge](https://anaconda.org/conda-forge/nd2reader/badges/downloads.svg)](https://anaconda.org/conda-forge/nd2reader)\n[![Build status](https://github.com/rbnvrw/nd2reader/actions/workflows/python-package.yml/badge.svg)](https://github.com/rbnvrw/nd2reader/actions/workflows/python-package.yml)\n\n### About\n\n`nd2reader` is a pure-Python package that reads images produced by NIS Elements 4.0+. It has only been definitively tested on NIS Elements 4.30.02 Build 1053. Support for older versions is being actively worked on.\nThe reader is written in the [pims](https://github.com/soft-matter/pims) framework, enabling easy access to multidimensional files, lazy slicing, and nice display in IPython.\n\n### Alternatives\n\n- [nd2](https://pypi.org/project/nd2/)\n- Open a PR if you'd like to be listed here.\n\n### Documentation\n\nThe documentation is available [here](https://open-science-tools.github.io/nd2reader/).\n\n### Installation\n\nThe package is available on PyPi. Install it using:\n\n```\npip install nd2reader\n```\n\nIf you don't already have the packages `numpy`, `pims`, `six` and `xmltodict`, they will be installed automatically if you use the `setup.py` script.\nPython \u003e= 3.5 are supported.\n\n#### Installation via Conda Forge\n\nInstalling `nd2reader` from the `conda-forge` channel can be achieved by adding `conda-forge` to your channels with:\n\n```\nconda config --add channels conda-forge\n```\n\nOnce the `conda-forge` channel has been enabled, `nd2reader` can be installed with:\n\n```\nconda install nd2reader\n```\n\nIt is possible to list all of the versions of `nd2reader` available on your platform with:\n\n```\nconda search nd2reader --channel conda-forge\n```\n\n### ND2s\n\n`nd2reader` follows the [pims](https://github.com/soft-matter/pims) framework. To open a file and show the first frame:\n\n```python\nfrom nd2reader import ND2Reader\nimport matplotlib.pyplot as plt\n\nwith ND2Reader('my_directory/example.nd2') as images:\n  plt.imshow(images[0])\n```\n\nAfter opening the file, all `pims` features are supported. Please refer to the [pims documentation](http://soft-matter.github.io/pims/).\n\n#### Backwards compatibility\n\nOlder versions of `nd2reader` do not use the `pims` framework. To provide backwards compatibility, a legacy [Nd2](https://open-science-tools.github.io/nd2reader/nd2reader.html#module-nd2reader.legacy) class is provided.\n\n### Contributing\n\nIf you'd like to help with the development of nd2reader or just have an idea for improvement, please see the [contributing](https://github.com/rbnvrw/nd2reader/blob/master/CONTRIBUTING.md) page\nfor more information.\n\n### Bug Reports and Features\n\nIf this fails to work exactly as expected, please open an [issue](https://github.com/rbnvrw/nd2reader/issues).\nIf you get an unhandled exception, please paste the entire stack trace into the issue as well.\n\n### Acknowledgments\n\nPIMS modified version by Ruben Verweij.\n\nOriginal version by Jim Rybarski. Support for the development of this package was partially provided by the [Finkelstein Laboratory](http://finkelsteinlab.org/).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FOpen-Science-Tools%2Fnd2reader","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FOpen-Science-Tools%2Fnd2reader","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FOpen-Science-Tools%2Fnd2reader/lists"}