{"id":24310313,"url":"https://github.com/nvladimus/npy2bdv","last_synced_at":"2025-04-13T04:46:19.261Z","repository":{"id":40957165,"uuid":"203410946","full_name":"nvladimus/npy2bdv","owner":"nvladimus","description":"Fast writing of numpy 3d-arrays into HDF5 Fiji/BigDataViewer files.","archived":false,"fork":false,"pushed_at":"2024-08-22T10:26:53.000Z","size":4328,"stargazers_count":35,"open_issues_count":2,"forks_count":12,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-04-13T04:46:12.434Z","etag":null,"topics":["bigdataviewer","h5","hdf5","numpy"],"latest_commit_sha":null,"homepage":"","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/nvladimus.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","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":"2019-08-20T16:10:51.000Z","updated_at":"2024-11-14T09:52:40.000Z","dependencies_parsed_at":"2023-12-20T06:51:25.977Z","dependency_job_id":"4d505e29-5241-449e-8e25-62648c3757aa","html_url":"https://github.com/nvladimus/npy2bdv","commit_stats":{"total_commits":110,"total_committers":4,"mean_commits":27.5,"dds":0.0636363636363636,"last_synced_commit":"f1f4f7b33ad13dd132d51f183a27428041b79686"},"previous_names":[],"tags_count":8,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nvladimus%2Fnpy2bdv","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nvladimus%2Fnpy2bdv/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nvladimus%2Fnpy2bdv/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nvladimus%2Fnpy2bdv/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nvladimus","download_url":"https://codeload.github.com/nvladimus/npy2bdv/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248665779,"owners_count":21142123,"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":["bigdataviewer","h5","hdf5","numpy"],"created_at":"2025-01-17T06:11:14.031Z","updated_at":"2025-04-13T04:46:19.227Z","avatar_url":"https://github.com/nvladimus.png","language":"Python","funding_links":["https://www.paypal.com/paypalme/NikitaVladimirov"],"categories":[],"sub_categories":[],"readme":"# npy2bdv\n A library for writing/reading HDF5/XML datasets of \n Fiji BigDataViewer/BigStitcher format as numpy arrays. \n \n[![Python 3.6](https://img.shields.io/badge/python-3.6-blue.svg)](https://www.python.org/downloads/release/python-360/)\n[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)\n \n ## Installation\n Run `pip install npy2bdv` in the command line. Use `import npy2bdv` in the code.\n \n ## Documentation\nFor a quick start, see examples in the Jupyter \n[`notebook`](/docs/examples/examples_h5writing.ipynb).\n\nAPI [documentation](https://nvladimus.github.io/npy2bdv/).\n\n ## Supported H5/XML writing options\n * compression methods `None`, `gzip`, `lzf` (`None` by default).\n * downsampling options: \n    - any number of mipmap levels\n    - computed via averaging, compatible with BigDataViewer/BigStitcher convention.\n * user-defined block sizes for H5 storage (default `4,256,256`)\n * any number of time points, illuminations, channels, tiles, angles.\n * arbitrary affine transformation for each individual view (e.g. translation, rotation, shear).\n * arbitrary voxel calibration for each view, to account for spatial anisotropy.\n * individual views can differ in dimensions, voxel size, voxel units, exposure time, and exposure units.\n * missing views are labeled in XML automatically.\n * support of additional meta-information:\n    - camera properties: `name`, `exposureTime`, `exposureUnits`\n    - `microscope` (name and version), `user`\n * writing virtual stacks of arbitrary size, by plane or sub-stack. Handy when your stack is larger than your RAM.\n    - virtual stacks can be written with multiple subsampling levels and compression.\n    \n ## New features\n See [Recent changes](CHANGELOG.md)\n \n ## Writing speed\n Currently speeds betewen 150 - 320 MB/s were achieved with confidence. Speeds of up to 2300 MB/s reported in earlier versions are likely due to bugs in testing methods in notebook [`examples_h5writing.ipynb`](/docs/examples/examples_h5writing.ipynb). More tesing is underway.\n\n ## Acknowledgements\n This code was inspired by [Talley Lambert's](https://github.com/tlambert03/imarispy) code \n and improved by generous input from Adam Glaser, [VolkerH](https://github.com/VolkerH), Doug Shepherd, \n [Peter H](https://github.com/abred), [Mike Taormina](https://github.com/miketaormina) and [Pradeep Rajasekhar](https://github.com/pr4deepr).\n \n To report issues or bugs please use the [issues](https://github.com/nvladimus/npy2bdv/issues) tool.\n \n ## Citation\n You can cite it like so\n \n [![DOI](https://zenodo.org/badge/203410946.svg)](https://zenodo.org/badge/latestdoi/203410946)\n\n## Support\nIf you find this library useful, send me some love :blush:\n\n\u003ca href=\"https://www.paypal.com/paypalme/NikitaVladimirov\"\u003e\u003cimg src=\"/assets/donate-paypal-button-blue.svg\" height=\"72\"\u003e\u003c/a\u003e\n\nIt will give me some dopamine and motivation to keep improving it :heart: \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnvladimus%2Fnpy2bdv","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnvladimus%2Fnpy2bdv","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnvladimus%2Fnpy2bdv/lists"}