{"id":17343482,"url":"https://github.com/lauraluebbert/thorimage-sync_2p-analysis","last_synced_at":"2025-03-27T09:41:46.769Z","repository":{"id":96700104,"uuid":"464707604","full_name":"lauraluebbert/ThorImage-Sync_2P-analysis","owner":"lauraluebbert","description":"Notebook to analyze ThorImage + ThorSync 2-photon data with light stimulation.","archived":false,"fork":false,"pushed_at":"2022-05-13T21:42:00.000Z","size":60,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-02-01T14:30:19.107Z","etag":null,"topics":["2-photon","calcium-imaging","image-processing","thorimage","thorsync"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","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/lauraluebbert.png","metadata":{"files":{"readme":"README.md","changelog":null,"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}},"created_at":"2022-03-01T01:51:55.000Z","updated_at":"2023-07-04T18:32:39.000Z","dependencies_parsed_at":null,"dependency_job_id":"0364f2fb-df26-4976-8c4a-a5ddb005163f","html_url":"https://github.com/lauraluebbert/ThorImage-Sync_2P-analysis","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lauraluebbert%2FThorImage-Sync_2P-analysis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lauraluebbert%2FThorImage-Sync_2P-analysis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lauraluebbert%2FThorImage-Sync_2P-analysis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lauraluebbert%2FThorImage-Sync_2P-analysis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lauraluebbert","download_url":"https://codeload.github.com/lauraluebbert/ThorImage-Sync_2P-analysis/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245820442,"owners_count":20677835,"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":["2-photon","calcium-imaging","image-processing","thorimage","thorsync"],"created_at":"2024-10-15T16:09:30.974Z","updated_at":"2025-03-27T09:41:46.764Z","avatar_url":"https://github.com/lauraluebbert.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# ThorImage/ThorSync_2P-analysis\n[![DOI](https://zenodo.org/badge/275931002.svg)](https://zenodo.org/badge/latestdoi/275931002)  \nNotebook to synchronize and analyze ThorImage + ThorSync 2-photon calcium imaging data with light stimulation.  \n\nThe notebook requires the user to draw ROIs as described [here](https://github.com/lauraluebbert/confocal_z-stack_analysis/blob/master/README.md). The ROIs are drawn on an automatically computed sum projection. The stimulation information is automatically obtained from the ThorSync file.\n\n# Output returned by notebook:\n\n### 1. Dataframe containing information per frame in the format:\n\nChannel + Sample\t | Filename\t        | Frame\t|Mean pixel value in ROI | Mean pixel value in bkg area |\tNorm_mean_pixel_value_in_ROI |\tTime passed (s) |\tdF/F0\t| LED (ON/OFF)|\n-------------------|------------------|-------|------------------------|------------------------------|------------------------------|------------------|-------|-------------|\nChanA (001_001_001)| ChanA_001_001_001|\t1.0\t  |542.6812468577175\t     | 541.7430997876858\t          |0.9381470700317323.           |\t0.0             |\t0.95  |\t0           |\n. . .              | . . .            |\t. . . |. . .\t                 | . . .\t                      |. . .\t                       |\t. . .           |\t. . .\t| . . .       |\n\n### 2. Pickled dictionary containing raw and analyzed data, including ROI coordinates\n\n### 3. dF/F0 over time showing stimulation:\n![R72A10-Chrimson_R52G12-GCaMP5_i003_df-f0](https://user-images.githubusercontent.com/56094636/156092081-a81363a3-789d-4090-9104-e7ad5bd791df.png)\nThe notebook also returns raw mean and background normalized mean traces.\n\n### 4. dF/F0 heatmap (sum over all frames):\n![2020-11-13_R70H05GCaMP_R72A10Chrim+ATR_thor6_df-f0_heatmap](https://user-images.githubusercontent.com/56094636/156091730-463c4883-5d9b-494a-944d-a6a562c62710.png)\n\n### 5. dF/F0 heatmap movie over time showing stimulation:\nhttps://user-images.githubusercontent.com/56094636/156097148-af4bfca4-12b5-4a44-889d-0c9e73c04b46.mp4\n\n### 6. ROIs drawn for area of interest and background:\n![2020-11-13_R70H05GCaMP_R72A10Chrim+ATR_thor6_rois_0](https://user-images.githubusercontent.com/56094636/156091221-d2ebeef5-7a64-40b5-a63c-8d4f2858223c.png)\n![2020-11-13_R70H05GCaMP_R72A10Chrim+ATR_thor6_bkg_rois_0](https://user-images.githubusercontent.com/56094636/156091196-315b928f-a331-4093-9131-3eda1ace2a77.png)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flauraluebbert%2Fthorimage-sync_2p-analysis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flauraluebbert%2Fthorimage-sync_2p-analysis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flauraluebbert%2Fthorimage-sync_2p-analysis/lists"}