{"id":19091957,"url":"https://github.com/allencellmodeling/timelapse_tools","last_synced_at":"2025-10-30T01:41:22.453Z","repository":{"id":91697905,"uuid":"221067345","full_name":"AllenCellModeling/timelapse_tools","owner":"AllenCellModeling","description":"Load and convert 🎥","archived":false,"fork":false,"pushed_at":"2021-10-27T18:57:23.000Z","size":40077,"stargazers_count":0,"open_issues_count":1,"forks_count":0,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-01-02T23:14:20.921Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/AllenCellModeling.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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":"2019-11-11T20:47:53.000Z","updated_at":"2020-01-08T22:27:39.000Z","dependencies_parsed_at":"2023-03-05T04:30:51.402Z","dependency_job_id":null,"html_url":"https://github.com/AllenCellModeling/timelapse_tools","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/AllenCellModeling%2Ftimelapse_tools","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenCellModeling%2Ftimelapse_tools/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenCellModeling%2Ftimelapse_tools/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenCellModeling%2Ftimelapse_tools/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/AllenCellModeling","download_url":"https://codeload.github.com/AllenCellModeling/timelapse_tools/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":240139500,"owners_count":19754124,"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":"2024-11-09T03:17:39.357Z","updated_at":"2025-10-30T01:41:17.382Z","avatar_url":"https://github.com/AllenCellModeling.png","language":"Python","readme":"# Timelapse Tools\n\n[![Build Status](https://github.com/AllenCellModeling/timelapse_tools/workflows/Build%20Master/badge.svg)](https://github.com/AllenCellModeling/timelapse_tools/actions)\n[![Documentation](https://github.com/AllenCellModeling/timelapse_tools/workflows/Documentation/badge.svg)](https://AllenCellModeling.github.io/timelapse_tools)\n[![Code Coverage](https://codecov.io/gh/AllenCellModeling/timelapse_tools/branch/master/graph/badge.svg)](https://codecov.io/gh/AllenCellModeling/timelapse_tools)\n\nLoad and convert timelapse CZI files to movie formats\n\n---\n\n## Features\n* Generate movies function that can operate on the `T` or `Z` axis\n* General purpose CZI delayed reader\n* Supported output formats:\n    * `mov`\n    * `avi`\n    * `mpg`\n    * `mpeg`\n    * `mp4`\n    * `mkv`\n    * `wmv`\n\n## Quick Start\n\n_**Read and interact with a large file:**_\n```python\nfrom timelapse_tools import daread\n\n# Dask array with delayed reads for every YX plane\nimg = daread(\"my_very_large_image.czi\")\n```\n\n_**Generate all scene and channel movie pairs from a file:**_\n```python\nfrom timelapse_tools import generate_movies\n\n# Generates a folder with every scene and channel pair of movies in the file\ngenerate_movies(\"my_very_large_image.czi\")\n```\n\n## Distributed\nIf you want to generate these movies in a distributed fashion, spin up a Dask scheduler.\nThe following settings generally work pretty well for our (AICS) SLURM cluster:\n```python\nfrom dask_jobqueue import SLURMCluster\nimport dask, dask.distributed\n\ncluster = SLURMCluster(\n    cores=2,\n    memory=\"16GB\",\n    walltime=\"12:00:00\",\n    queue=\"aics_cpu_general\"\n)\ncluster.adapt(minimum_jobs=2, maximum_jobs=40)\nclient = dask.distributed.Client(cluster)\n```\n\nFrom there you simply need to pass the distributed executor port to the\n`generate_movies` function:\n```python\nfrom timelapse_tools import generate_movies\n\ngenerate_movies(\n    \"my_very_large_image.czi\",\n    distributed_executor_port=cluster.scheduler_info[\"address\"].split(\":\")[-1]\n)\n```\n\n_It is also recommended that whichever machine you run the scheduler on, to also set the\nfollowing environment variable:_\n```bash\nexport DASK_DISTRIBUTED__SCHEDULER__WORK_STEALING=\"False\"\n```\n_More details under the \"work stealing\" section\n[here](https://docs.prefect.io/core/tutorials/dask-cluster.html)._\n\n## Installation\n\n`pip install git+https://github.com/AllenCellModeling/timelapse_tools.git`\n\n_*Note:* If you want to produce workflow visualizations at the end of conversion, you\nwill need to install pydot + graphviz._\n\n## Documentation\nFor full package documentation please visit [AllenCellModeling.github.io/timelapse_tools](https://AllenCellModeling.github.io/timelapse_tools).\n\nLicense: Allen Institute Software License\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fallencellmodeling%2Ftimelapse_tools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fallencellmodeling%2Ftimelapse_tools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fallencellmodeling%2Ftimelapse_tools/lists"}