Metadata-Version: 2.1
Name: actk
Version: 0.1.1
Summary: Automated Cell Toolkit
Home-page: https://github.com/AllenCellModeling/actk
Author: Jackson Maxfield Brown
Author-email: jacksonb@alleninstitute.org
License: Allen Institute Software License
Description: # actk
        
        [![Build Status](https://github.com/AllenCellModeling/actk/workflows/Build%20Master/badge.svg)](https://github.com/AllenCellModeling/actk/actions)
        [![Documentation](https://github.com/AllenCellModeling/actk/workflows/Documentation/badge.svg)](https://AllenCellModeling.github.io/actk)
        [![Code Coverage](https://codecov.io/gh/AllenCellModeling/actk/branch/master/graph/badge.svg)](https://codecov.io/gh/AllenCellModeling/actk)
        
        Automated Cell Toolkit
        
        ---
        
        A pipeline to process field-of-view (FOV) microscopy images and generate data and
        render-ready products for the cells in each field. Of note, the data produced by this
        pipeline is used for the [Cell Feature Explorer](https://cfe.allencell.org/).
        
        ## Features
        All steps and functionality in this package can be run as single steps or all together
        by using the command line.
        
        In general, all commands for this package will follow the format:
        `actk {step} {command}`
        
        * `step` is the name of the step, such as "StandardizeFOVArray" or "SingleCellFeatures"
        * `command` is what you want that step to do, such as "run" or "push"
        
        Each step will check that the dataset provided contains the required fields prior to
        processing. For details and definitions on each field, see our
        [dataset fields documentation](https://AllenCellModeling.github.io/actk/dataset_fields.html).
        
        An example dataset can be seen [here](https://open.quiltdata.com/b/aics-modeling-packages-test-resources/tree/actk/test_data/data/example_dataset.csv).
        
        ### Pipeline
        To run the entire pipeline from start to finish you can simply run:
        
        ```bash
        actk all run --dataset {path to dataset}
        ```
        
        Step specific parameters can additionally be passed by simply appending them.
        For example: the step `SingleCellFeatures` has a parameter for
        `cell_ceiling_adjustment` and this can be set on both the individual step run level and
        also for the entire pipeline with:
        
        ```bash
        actk all run --dataset {path to dataset} --cell_ceiling_adjustment {integer}
        ```
        
        To run in distributed mode across the SLURM cluster at AICS you can add the
        `--distributed` flag to the pipeline call.
        
        To set distributed cluster and worker parameters you can additionally add the flags:
        * `--n_workers {int}` (i.e. `--n_workers 100`)
        * `--worker_cpu {int}` (i.e. `--worker_cpu 2`)
        * `--worker_mem {str}` (i.e. `--worker_mem 100GB`)
        
        ### Individual Steps
        * `actk standardizefovarray run --dataset {path to dataset}`, Generate standardized,
        ordered, and normalized FOV images as OME-Tiffs.
        * `actk singlecellfeatures run --dataset {path to dataset}`, Generate a features JSON
        file for each cell in the dataset.
        
        ## Installation
        **Install Requires:** The python package, `numpy`, must be installed prior to the
        installation of this package: `pip install numpy`
        
        **Stable Release:** `pip install actk`<br>
        **Development Head:** `pip install git+https://github.com/AllenCellModeling/actk.git`
        
        ## Documentation
        For full package documentation please visit
        [allencellmodeling.github.io/actk](https://allencellmodeling.github.io/actk/index.html).
        
        ## Development
        See
        [CONTRIBUTING.md](https://github.com/AllenCellModeling/actk/blob/master/CONTRIBUTING.md)
        for information related to developing the code.
        
        For more details on how this pipeline is constructed please see
        [cookiecutter-stepworkflow](https://github.com/AllenCellModeling/cookiecutter-stepworkflow)
        and [datastep](https://github.com/AllenCellModeling/datastep).
        
        To add new steps to this pipeline, run `make_new_step` and follow the instructions in
        [CONTRIBUTING.md](https://github.com/AllenCellModeling/actk/blob/master/CONTRIBUTING.md)
        
        ### Developer Installation
        The following two commands will install the package with dev dependencies in editable
        mode and download all resources required for testing.
        
        ```bash
        pip install -e .[dev]
        python scripts/download_test_data.py
        ```
        
        ### AICS Developer Instructions
        If you want to run this pipeline with the Pipeline Integrated Cell dataset
        (`pipeline 4.*`) run the following commands:
        
        ```bash
        pip install -e .[all]
        python scripts/download_aics_dataset.py
        ```
        
        Options for this script are available and can be viewed with:
        `python scripts/download_aics_dataset.py --help`
        
        ***Free software: Allen Institute Software License***
        
Keywords: actk,computational biology,workflow,cell,microscopy
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: Free for non-commercial use
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Provides-Extra: setup
Provides-Extra: test
Provides-Extra: dev
Provides-Extra: aics
Provides-Extra: all
