Downloads
=========

This page contains downloadable scripts, notebooks, and utilities for PhenoTypic.

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    .. grid-item-card:: phenotypic-cli.py
        :shadow: md

        Backwards compatibility wrapper for phenotypic-cli.py.

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        :download:`Download script <_downloads/phenotypic-cli.py>`

    .. grid-item-card:: SLURM Job Chain Manager for Image Processing
        :shadow: md

        Processes multiple directories sequentially with dependencies USAGE With directory file

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        :download:`Download script <_downloads/phenotypic-slurm.sh>`


Downloadable Notebooks
======================

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    .. grid-item-card:: 1. Getting Started
        :shadow: md

        Get started with image processing in PhenoTypic.

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        :download:`Download notebook <user_guide/tutorial/notebooks/GettingStarted.ipynb>`

    .. grid-item-card:: 4. Working with GridImage: Grid-Specific Features
        :shadow: md

        This tutorial focuses on `GridImage` - a specialized class for analyzing arrayed microbe colonies on solid media agar plates.

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        :download:`Download notebook <user_guide/tutorial/notebooks/GridImages.ipynb>`

    .. grid-item-card:: 6. Fitting Logistic Growth Curves
        :shadow: md

        ---

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        :download:`Download notebook <user_guide/tutorial/notebooks/GrowthCurves.ipynb>`

    .. grid-item-card:: 5. Make your own `ImagePipeline`
        :shadow: md

        For a more detailed explanation on the components of `phenotypic.Image` and `phenotypic.GridImage`, see the {doc} `Images` and {doc} `GridImages` tutorial.

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        :download:`Download notebook <user_guide/tutorial/notebooks/ImagePipelines.ipynb>`

    .. grid-item-card:: 3. Understanding the Image Class: Data Components and Accessors
        :shadow: md

        This tutorial provides a comprehensive guide to the PhenoTypic `Image` class architecture, focusing on its main data components and how they interact with detection and analysis modules.

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        :download:`Download notebook <user_guide/tutorial/notebooks/Images.ipynb>`

    .. grid-item-card:: 2. Using `ImagePipeline`s to process batches
        :shadow: md

        Learn to tune and use prefabricated image processing pipelines, then deploy them at scale.

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        :download:`Download notebook <user_guide/tutorial/notebooks/LongerStart.ipynb>`