{"id":19034841,"url":"https://github.com/int-brain-lab/viewephys","last_synced_at":"2025-04-23T17:47:12.167Z","repository":{"id":55585687,"uuid":"458768788","full_name":"int-brain-lab/viewephys","owner":"int-brain-lab","description":"Neuropixel raw data viewer","archived":false,"fork":false,"pushed_at":"2024-12-06T17:51:01.000Z","size":2043,"stargazers_count":3,"open_issues_count":4,"forks_count":0,"subscribers_count":25,"default_branch":"main","last_synced_at":"2025-04-13T05:22:55.462Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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/int-brain-lab.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":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2022-02-13T09:53:28.000Z","updated_at":"2024-12-06T17:50:47.000Z","dependencies_parsed_at":"2024-04-19T17:33:10.033Z","dependency_job_id":"086bffe9-ab89-41d7-baac-31f8b83755e3","html_url":"https://github.com/int-brain-lab/viewephys","commit_stats":null,"previous_names":["oliche/viewephys"],"tags_count":5,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/int-brain-lab%2Fviewephys","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/int-brain-lab%2Fviewephys/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/int-brain-lab%2Fviewephys/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/int-brain-lab%2Fviewephys/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/int-brain-lab","download_url":"https://codeload.github.com/int-brain-lab/viewephys/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":250485046,"owners_count":21438353,"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":"2024-11-08T21:47:41.984Z","updated_at":"2025-04-23T17:47:12.150Z","avatar_url":"https://github.com/int-brain-lab.png","language":"Python","readme":"# viewephys\nNeuropixel raw data viewer\n\n## Installation\n`pip install viewephys`\n\nAlternatively, in development mode:\n```shell\ngit clone https://github.com/int-brain-lab/viewephys.git\ncd viewephys\npip install -e .\n```\n\n### Supported environments\nThis is compatible with the [IBL environment](https://github.com/int-brain-lab/iblenv)\n\nOtherwise, you can create a new environment as such:\n```shell\nconda create -n viewephys python=3.12\nconda activate viewephys\n```\nAnd then follow the install instructions above.\n\n## Controls\n- `ctrl + z`: -3dB gain\n- `ctrl + a`: +3dB gain\n- `ctrl + p`: in multi-windows mode, link the displays (pan, zoom and gain)\n\n### Pick spikes\nWhen the picking mode is enabled (menu pick)\n- left button click sets a point\n- shift + left button removes a point\n- control + left does not wrap on maximum around pick\n- space increments the spike group number\n\n\n## Examples\n\n### Visualize raw binary file\nActivate your environment and type `viewephys`, you can then load a neuropixel binary file using the file menu.\n\n![alt text](./docs/raw_bin_viewer_destripe.png \"Ephys viewer \")\n\nAlternatively you can point the viewer to a specific file using the command line:\n```shell\nviewphys -f /path/to/raw.bin\n```\n\n### Load in a numpy array or slice\n```python\n# if running ipython, you may have to use the `%gui qt` magic command\nimport numpy as np\nfrom viewephys.gui import viewephys\nnc, ns, fs = (384, 50000, 30000)  # this mimics one second of neuropixel data\ndata = np.random.randn(nc, ns) / 1e6  # volts by default\nve = viewephys(data, fs=fs)\n```\n![alt text](./docs/view_rand_array.png \"Ephys viewer\")\n    \n\n## Contribution\nFork and PR.\n\nPypi Release checklist:\n```shell\nruff check\nrm -fR dist\nrm -fR build\npython setup.py sdist bdist_wheel\ntwine upload dist/*\n#twine upload --repository-url https://test.pypi.org/legacy/ dist/*\n```\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fint-brain-lab%2Fviewephys","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fint-brain-lab%2Fviewephys","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fint-brain-lab%2Fviewephys/lists"}