{"id":19091976,"url":"https://github.com/allencellmodeling/polar_express","last_synced_at":"2025-02-22T07:27:45.131Z","repository":{"id":91697847,"uuid":"279960539","full_name":"AllenCellModeling/polar_express","owner":"AllenCellModeling","description":"Distributed DataStep pipeline to process 3D microscopy images, perform large-scale statistical analysis, and generate summary visualizations for the 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polar_express\n\n[![Build Status](https://github.com/AllenCellModeling/polar_express/workflows/Build%20Master/badge.svg)](https://github.com/AllenCellModeling/polar_express/actions)\n[![Documentation](https://github.com/AllenCellModeling/polar_express/workflows/Documentation/badge.svg)](https://AllenCellModeling.github.io/polar_express)\n[![Code Coverage](https://codecov.io/gh/AllenCellModeling/polar_express/branch/master/graph/badge.svg)](https://codecov.io/gh/AllenCellModeling/polar_express)\n\nPolar Express: 3D Image Analysis Pipeline\n\n---\n\nA DataStep pipeline to process 3D single-cell microscopy images, perform large-scale statistical analysis on GFP intensity distribution for target organelles, and generate summary visualizations for the data.\n\n## Features\nAll steps and functionality in this package can be run as single steps or all together\nby using the command line.\n\nIn general, all commands for this package will follow the format:\n`polar_express {step} {command}`\n\n* `step` is the name of the step, such as \"selectdata\" or \"computecellmetrics\"\n* `command` is what you want that step to do, such as \"run\" or \"push\"\n\nExample datasets can be accessed [here](https://open.quiltdata.com/b/allencell).\n\n### Pipeline\nTo run the entire pipeline from start to finish you can simply run:\n\n```bash\npolar_express all run --dataset {path to dataset}\n```\n\nStep specific parameters can additionally be passed by simply appending them.\nFor example: the step `computecellmetrics` has a parameter for\n`num_angular_compartments` and this can be set on both the individual step run level and\nalso for the entire pipeline with:\n\n```bash\npolar_express all run --dataset {path to dataset} --num_angular_compartments {integer}\n```\n\nSee the [steps module in our documentation](https://allencellmodeling.github.io/polar_express/polar_express.steps.html)\nfor a full list of parameters for each step\n\n#### Pipeline Config\n\nA configuration file can be provided to the underlying `datastep` library that manages\nthe data storage and upload of the steps in this workflow.\n\nThe config file should simply be called `workflow_config.json` and be available from\nwhichever directory you run `polar_express` from. If this config is not found in the current\nworking directory, defaults are selected by the `datastep` package.\n\nHere is an example of our production config:\n\n```json\n{\n    \"quilt_storage_bucket\": \"s3://allencell\",\n    \"project_local_staging_dir\": \"/allen/aics/modeling/william.chen/results/polar_express\"\n}\n```\n\nYou can even additionally attach step-specific configuration in this file by using the\nname of the step like so:\n\n```json\n{\n    \"quilt_storage_bucket\": \"s3://example_config_7\",\n    \"project_local_staging_dir\": \"example/config/7\",\n    \"example\": {\n        \"step_local_staging_dir\": \"example/step/local/staging/\"\n    }\n}\n```\n\n### Individual Steps\n* `polar_express selectdata run --dataset {path to dataset}`, Load 3D cell images\nfiltered for the target structure or organelle, or alternatively, generate artificial cells.\n* `polar_express computecellmetrics run`, Compute and save key metrics relating to the\nstructure of the cell and GFP distribution.\n* `polar_express gathertestvisualize run`, Generate visualizations for the compartmentalized\nGFP distributions, including polar heatmaps, and run statistical tests over the entire dataset.\n\n## Installation\n**Install Requires:** The python package, `numpy`, must be installed prior to the\ninstallation of this package: `pip install numpy`\n\n**Stable Release:** `pip install polar_express`\u003cbr\u003e\n**Development Head:** `pip install git+https://github.com/AllenCellModeling/polar_express.git`\n\n## Documentation\nFor full package documentation please visit\n[allencellmodeling.github.io/polar_express](https://allencellmodeling.github.io/polar_express/index.html).\n\n## Development\nSee [CONTRIBUTING.md](CONTRIBUTING.md) for information related to developing the code.\n\nFor more details on how this pipeline is constructed please see\n[cookiecutter-stepworkflow](https://github.com/AllenCellModeling/cookiecutter-stepworkflow)\nand [datastep](https://github.com/AllenCellModeling/datastep).\n\nTo add new steps to this pipeline, run `make_new_step` and follow the instructions in\n[CONTRIBUTING.md](CONTRIBUTING.md)\n\n### Developer Installation\nThe following two commands will install the package with dev dependencies in editable\nmode and download all resources required for testing.\n\n```bash\npip install -e .[dev]\npython scripts/download_test_data.py\n```\n\n***Free software: Allen Institute Software License***\n\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fallencellmodeling%2Fpolar_express","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fallencellmodeling%2Fpolar_express","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fallencellmodeling%2Fpolar_express/lists"}