PyPl8 1.0.1

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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(). This function renames a folder of images by matching the barcode visible in each image to information provided in an excel spreadsheet. 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 function ProcessImage() for processing a single image and the functions ProcessBatch() and ParallelProcessBatch() for processing a folder of images with the same settings.

• The package contains 3 example images,Funnel(), PSAT1(), and OTC(), which can be used to test out the package. The function ProcessImageTest(), processes images already loaded into the workspace as arrays as the example images would be.

• To check which version of PyPl8 you have installed run

    import PyPl8
    PyPl8.__version__

Examples

Please visit the PyPl8 github page to see examples and more detailed documentation.