{"id":25603485,"url":"https://github.com/jeffshee/cell-rotation","last_synced_at":"2025-11-10T22:30:54.911Z","repository":{"id":45849742,"uuid":"401221170","full_name":"jeffshee/cell-rotation","owner":"jeffshee","description":null,"archived":false,"fork":false,"pushed_at":"2021-12-02T05:45:28.000Z","size":27088,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-02-14T03:56:19.797Z","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":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/jeffshee.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}},"created_at":"2021-08-30T04:58:56.000Z","updated_at":"2021-12-02T05:05:59.000Z","dependencies_parsed_at":"2022-08-30T13:40:11.414Z","dependency_job_id":null,"html_url":"https://github.com/jeffshee/cell-rotation","commit_stats":null,"previous_names":[],"tags_count":6,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jeffshee%2Fcell-rotation","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jeffshee%2Fcell-rotation/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jeffshee%2Fcell-rotation/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jeffshee%2Fcell-rotation/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/jeffshee","download_url":"https://codeload.github.com/jeffshee/cell-rotation/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":240057119,"owners_count":19741246,"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":"2025-02-21T17:27:07.851Z","updated_at":"2025-11-10T22:30:54.849Z","avatar_url":"https://github.com/jeffshee.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Cell Rotation\nPython script to calculate the rotation speed of the cell from cell videos.\n\n## Dependency\n```\npython3\npip install tqdm seaborn scikit-learn scipy Pillow pandas opencv-python opencv-contrib-python numpy matplotlib\n```\n\n## Usage\n0. Get your system ready for the mentioned dependencies.\n1. Clone this repo.\n2. Inside the script directory, create a new directory named `dataset`.\n3. Copy the cell videos to analyze into the `dataset` directory.\n4. Execute the main script, `python main.py`.\n\n## Start analyzing\n1. **Select ROI for analyzing**  \nThe selection will be cached into python pickle file named `roi.pkl`, so that you wouldn't need to select the ROI again next time for the same video. Press ENTER to proceed.\n2. **Adjust the threshold for the binarization**  \nThe optimal threshold gives the most accurate cell area. Press ENTER to proceed.\n   ![](res/gui_roi_thresh.gif)\n3. The processing will be started. The results will be outputted into the directory named `output`.\n\n## Output\nThe output result is a heatmap of pairwise similarity of frame `t1` and frame `t2`. For example,\n\n![](res/rotate-qr-320-crop-fig-a-3.0s.png)\n\nFrom this figure, we can observe some peaks in pairwise similarity at `delta=30` and `delta=60`. These peaks indicate the rotation cycles. Given that the rotation cycle is `30 (frames)`, fps is `30.0`, we can calculate that the rotation speed is `360 (deg/s)`.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjeffshee%2Fcell-rotation","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjeffshee%2Fcell-rotation","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjeffshee%2Fcell-rotation/lists"}