{"id":18420596,"url":"https://github.com/openworm/wormsenselab_ash","last_synced_at":"2025-04-13T09:18:50.326Z","repository":{"id":145390662,"uuid":"400186040","full_name":"openworm/WormsenseLab_ASH","owner":"openworm","description":"Electrophysiological recordings of neuron ASH from Wormsense Lab","archived":false,"fork":false,"pushed_at":"2021-09-28T10:25:39.000Z","size":20856,"stargazers_count":3,"open_issues_count":1,"forks_count":0,"subscribers_count":13,"default_branch":"main","last_synced_at":"2025-04-13T09:18:45.637Z","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":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/openworm.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"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":"2021-08-26T13:51:28.000Z","updated_at":"2023-07-21T05:21:56.000Z","dependencies_parsed_at":null,"dependency_job_id":"9e060851-b99c-4128-bd51-c60dec510e4d","html_url":"https://github.com/openworm/WormsenseLab_ASH","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/openworm%2FWormsenseLab_ASH","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/openworm%2FWormsenseLab_ASH/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/openworm%2FWormsenseLab_ASH/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/openworm%2FWormsenseLab_ASH/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/openworm","download_url":"https://codeload.github.com/openworm/WormsenseLab_ASH/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248688562,"owners_count":21145769,"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":"2024-11-06T04:22:23.180Z","updated_at":"2025-04-13T09:18:50.305Z","avatar_url":"https://github.com/openworm.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Wormsense Lab Data - ASH\n\nElectrophysiological recordings of [ASH neuron](https://www.wormatlas.org/neurons/Individual%20Neurons/ASHframeset.html) from [Wormsense Lab](https://med.stanford.edu/goodmanlab.html) of Miriam Goodman.\n\nThis code uses a metadata spreadsheet and .dat files acquired from the HEKA Patchmaster software to generate NWB files with experimental data.\n\nExample converted data file shown here:\n\n\u003cimg src=\"images/example_goodman_lab_file.png\" width=\"1200\" /\u003e\n\n### How to use\n\nThe data can be converted by running the following command while in the src directory:\n\n```python\npython goodman_to_nwb_conversion.py\n```\n\nThis `goodman_to_nwb_conversion.py` file can be edited to convert additional datasets, overwrite existing files, or use other metadata spreadsheets (see example below).\n\n```python\n    metadata_filename = '..//test_data//ASH-metadata_12_III_29.xls'\n    cell_list = ['ASH097', 'ASH116', 'ASH230', 'ASH287']\n    overwrite = True\n\n    convert_goodman_to_nwb(metadata_filename, cell_list, overwrite)\n```\n\nThe x_to_nwb module used to convert .dat files to .nwb format was forked from [byte-physics/x_to_nwb](https://github.com/byte-physics/x-to-nwb) and adapted to be compatible with data acquired from older Patchmaster versions (pre v2x90). This module has also been adapted to support a metadata input that can be used to incorporate additional experiment information when generating the NWB file.\n\n### Current state of the project\n\nNote, data is in the process of being moved here from https://github.com/OpenSourceBrain/GSoC_2021_OSB_NWB.\n\nCurrent outstanding question and remaining to-do items for a fully converted dataset are described in the documentation: [doc/dat_to_nwb_testing.md](doc/dat_to_nwb_testing.md)\n\n### Example datasets\n\n\u003ca href=\"test_data/README.md\"\u003e\u003cimg src=\"test_data/09-03-31-1.png\"/\u003e\u003c/a\u003e\n\nA number of example converted datasets have been added to this repository [here](test_data/README.md).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopenworm%2Fwormsenselab_ash","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fopenworm%2Fwormsenselab_ash","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopenworm%2Fwormsenselab_ash/lists"}