PyPl8 1.0.0

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PyPl8

Image analysis package for segmenting images of microbial communities and extracting quantitative features automatically.

Background

This package makes use of the cv2 and sci-kit image libraries for image processing.

It was developed in the Dudley lab at Pacific Northwest Research Institute and is currently most useful for analyzing images of rectangularly arrayed patches/colonies on agar plates photographed against a dark background.

Organization

• PyPl8.BarcodeMethods contains the function Rename() which can be used to rename a folder of images based on the barcode visible in each image if an excel spreadsheet relating barcode numbers to relevant plate information is provided in the current working directory. Barcodes are detected using pyzbar. See their documentation for a list of recognizable barcode styles.

• PyPl8.PreprocessingMethods contains functions used to crop each image to relevant areas of interest prior to segmentation.

• ProcessImages.py contains the main functions for processing a single image, ProcessImage(), or a batch of images, ProcessBatch() and ParallelProcessBatch().

• There are several example images included in the package which can be used to test out the functions provided. These images are Funnel(), PSAT1(), and OTC(). There is only one test function provided, ProcessImageTest(), which can be used to process images already loaded into the workspace as arrays.

• To check which version of PyPl8 you have installed run

  import PyPl8 PyPl8.version

Examples

For more detailed documentation and to see examples of how to use these functions, visit the PyPl8 github page.