Computational protocol: Image Quality Ranking Method for Microscopy

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Protocol publication

[…] Our PyImageQualityRanking software was written in Python, and it is released under BSD open-source license. Only standard Scientific Python libraries (Numpy, SciPy, Pandas, Matplotlib) are utilized. Numpy and SciPy were used to implement all the image processing and analysis features, whereas Pandas was used to implement methods to process the results (data sorting by measure value, measure calculations, measure normalization etc.). Matplotlib was used for image visualization, as well as to produce mathematical plots. In many quantitative microscopy applications time lapse recordings are made, which means that the order of the images should not be changed – therefore the data sorting features in PyImageQualityRanking software do not actually change the order of the images, but instead the software creates a separate data file with the image names and measures, which can be safely modified, without risk of compromising the original image data. The basic functionality of the PyImageQualitRanking software is described in pseudocode in () . […]

Pipeline specifications

Software tools Numpy, matplotlib
Application Miscellaneous