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Project description
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.
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 omnitrays photographed against a dark background.
Organization
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The function in the barcode methods can be used to rename images based on a barcode visible in the image if an excel spreadsheet relating barcode numbers to relevant plate information is provided.
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The functions in the preprocessing methods are used to crop each image to relevant areas of interest
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ProcessImages.py contains the main functions for processing a single image or a batch of images
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Now includes parallel batch processing
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There are several example images included in the package which can be used for demos
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