nriss / imaging-tools

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usefulTools

Useful tools to get stats and look at tif images. All scripts can be used as a bash command is the folder is added to the $PATH

  • combineStack : combine two image stacks (USAGE : combineStack [imagePath] [imagePath2])
  • cropImage : crop image in 128.128 patches (USAGE : cropImage [imagePath] [options])
  • shiftTif : shift all images of a stack from n pixels on x and / or y axis (USAGE : shiftTif [imagePath] [options])
  • showPatches : quickly show 5 X and Y images of a npz stack patches (USAGE : showPatches [imagePath])
  • showTif : show tif images with pyplot (USAGE : showTif [imagePath] [options])
  • splitTif : split a tif stack in a smaller stack (USAGE : splitTif [imagePath] [options])

Each tool has a --help function for more information

About

This toolbox has been developped to help training CSBDeep models applied to multi dimensional super resolution microscopy (https://github.com/nriss/DatasetMicroscopy). Developped by Nicolas Riss under the supervision of Julien Godet

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