{"id":18420630,"url":"https://github.com/openworm/neuropal","last_synced_at":"2025-04-14T20:09:57.558Z","repository":{"id":145390422,"uuid":"383202045","full_name":"openworm/NeuroPAL","owner":"openworm","description":"Scripts to analyse and convert NeuroPAL datasets","archived":false,"fork":false,"pushed_at":"2023-11-21T14:17:38.000Z","size":11505,"stargazers_count":4,"open_issues_count":0,"forks_count":0,"subscribers_count":12,"default_branch":"main","last_synced_at":"2025-04-14T20:09:49.468Z","etag":null,"topics":["3d","celegans","neuroml","neuroscience","openworm"],"latest_commit_sha":null,"homepage":"https://www.opensourcebrain.org/projects/neuropal","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":"2021-07-05T16:26:50.000Z","updated_at":"2024-07-17T07:32:18.000Z","dependencies_parsed_at":null,"dependency_job_id":"5c7d75c6-3cb6-4ba5-9ffa-1a378d4a1b1a","html_url":"https://github.com/openworm/NeuroPAL","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%2FNeuroPAL","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/openworm%2FNeuroPAL/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/openworm%2FNeuroPAL/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/openworm%2FNeuroPAL/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/openworm","download_url":"https://codeload.github.com/openworm/NeuroPAL/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248952349,"owners_count":21188426,"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":["3d","celegans","neuroml","neuroscience","openworm"],"created_at":"2024-11-06T04:22:30.356Z","updated_at":"2025-04-14T20:09:57.526Z","avatar_url":"https://github.com/openworm.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# NeuroPAL\n\n[![Continuous builds](https://github.com/openworm/NeuroPAL/actions/workflows/omv-ci.yml/badge.svg)](https://github.com/openworm/NeuroPAL/actions/workflows/omv-ci.yml) [![Test Notebooks](https://github.com/openworm/NeuroPAL/actions/workflows/test-notebooks.yml/badge.svg)](https://github.com/openworm/NeuroPAL/actions/workflows/test-notebooks.yml)\n\nThis repository contains some test scripts which use the NeuroPAL datasets.\n\n**Note: Work in progress! Subject to change without notice! Please get in contact if you would like to reuse this dataset, to help improve the quality of the conversion**\n\n\n# Canonical positions and colors\n\nA canonical set of positions for the cell bodes as well as colors reflecting expression levels has been produced. A description of the data can be found in: **Toward a more accurate 3D atlas of \u003ci\u003eC. elegans\u003c/i\u003e neurons**, Michael Skuhersky, Tailin Wu, Eviatar Yemini, Amin Nejatbakhsh, Edward Boyden \u0026 Max Tegmark [BMC Bioinformatics volume 23, Article number: 195 (2022)](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-022-04738-3)\n\nMore details on the data can be found [here](data/CanonicalPositions/README.md), and a Jupyter notebook containing the conversion of this data to NeuroML is [here](https://github.com/openworm/NeuroPAL/blob/main/TestCanonicalPositions.ipynb).\n\n![Screenshot_Canonical.png](https://raw.githubusercontent.com/openworm/NeuroPAL/main/NeuroML2/Screenshot_Canonical.png)\n\n\u003cp align=\"center\"\u003e\u003ci\u003eThe above image shows the canonical positions and colors \u003ca href=\"https://v1.opensourcebrain.org/projects/neuropal/repository/revisions/main/show/NeuroML2?explorer=https%253A%252F%252Fraw.githubusercontent.com%252Fopenworm%252FNeuroPAL%252Fmain%252FNeuroML2%252FNeuroPAL_Canonical.net.nml\"\u003evisualised on Open Source Brain\u003c/a\u003e.\u003c/i\u003e\u003c/p\u003e\n\n\n# Head and tail datasets\n\nThe original publication on NeuroPAL was: Eviatar Yemini, Albert Lin, Amin Nejatbakhsh, Erdem Varol, Ruoxi Sun, Gonzalo E. Mena, Aravinthan D.T. Samuel, Liam Paninski, Vivek Venkatachalam, Oliver Hobert, \u003cb\u003eNeuroPAL: A Multicolor Atlas for Whole-Brain Neuronal Identification in \u003ci\u003eC. elegans\u003c/i\u003e\u003c/b\u003e,\n[Cell, Volume 184, Issue 1, 2021](https://doi.org/10.1016/j.cell.2020.12.012).\n\nThe dataset released with this publication on positions and colors (as used in Figures 2 and 7) of cells in the head and tail has been used in [this Jupyter notebook](https://github.com/openworm/NeuroPAL/blob/main/TestLoadingData.ipynb), and extracted from the Excel sheet, and converted to NeuroML format.\n\n![Screenshot_HM.png](https://raw.githubusercontent.com/openworm/NeuroPAL/main/NeuroML2/Screenshot_HM.png)\n\n\u003cp align=\"center\"\u003e\u003ci\u003eThe above image shows the data \u003ca href=\"https://v1.opensourcebrain.org/projects/neuropal/repository/revisions/main/show/NeuroML2?explorer=https%253A%252F%252Fraw.githubusercontent.com%252Fopenworm%252FNeuroPAL%252Fmain%252FNeuroML2%252FNeuroPAL_Herm_Male.net.nml\"\u003evisualised on Open Source Brain\u003c/a\u003e, with the data from the male worm shown in front (head to left, tail to right, shifted to be adjacent), and the equivalent hermaphrodite data behind.\u003c/i\u003e\u003c/p\u003e\n\n# Whole body datasets\n\nUpdated data has been provided by Michael Skuhersky on the whole body cell positions and colors. Conversion of this data can be seen [here](https://github.com/openworm/NeuroPAL/blob/main/TestWholeWorm.ipynb).\n\n![Screenshot_Whole.png](https://raw.githubusercontent.com/openworm/NeuroPAL/main/NeuroML2/Screenshot_Whole.png)\n\n\u003cp align=\"center\"\u003e\u003ci\u003eThe above image shows the whole worm data \u003ca href=\"https://v1.opensourcebrain.org/projects/neuropal/repository/revisions/main/show/NeuroML2?explorer=https%253A%252F%252Fraw.githubusercontent.com%252Fopenworm%252FNeuroPAL%252Fmain%252FNeuroML2%252FNeuroPAL_All_straightened.net.nml\"\u003evisualised on Open Source Brain\u003c/a\u003e. Seven worm reconstructions are shown, and the worm body/layout has been straightened/standardized as described \u003ca href=\"https://www.biorxiv.org/content/10.1101/2021.06.09.447813v1.full\"\u003ehere\u003c/a\u003e.\u003c/i\u003e\u003c/p\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopenworm%2Fneuropal","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fopenworm%2Fneuropal","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopenworm%2Fneuropal/lists"}