Downloads

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

phenotypic-cli.py

Backwards compatibility wrapper for phenotypic-cli.py.

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SLURM Job Chain Manager for Image Processing

Processes multiple directories sequentially with dependencies USAGE With directory file

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Downloadable Notebooks

1. Getting Started

Get started with image processing in PhenoTypic.

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4. Working with GridImage: Grid-Specific Features

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

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6. Fitting Logistic Growth Curves

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5. Make your own ImagePipeline

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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3. Understanding the Image Class: Data Components and Accessors

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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2. Using `ImagePipeline`s to process batches

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

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