yafft, a flatfield correction tool for micrographs

 

yafft means ‚just another flatfield tool‘. It is written in python and is intended to help in a flatfield correction of micrographs (images that are taken through a microscope). The program is published under the
GNU GENERAL PUBLIC LICENSE, Version 3, 29 June 2007
https://www.gnu.org/licenses/gpl-3.0.txt

It works in the following way:

First specify the flatfield frame(s) in the first file input dialog. These frames are called ‚flats‘. It is possible to use one or more flatfield frames. In case of more than one frame these frames are averaged by the program and the averaged image will be used for correction.

Second specify in the second file input dialog the frames that must be corrected. These frames are called ‚lights‘. You can use one ore more frames.

Third specify the variable ’sigma‘. It is used to blur the flat frame. Without this step the resulting image will be unintentionally sharpened. The higher the value of sigma the more the flat frame will be blured and the the light frame will be less corrected. For most cases a value between 2 and 10 is good.

In the file input dialogs you are able to load .jpg, .tif or raw files (.nef, .cr2). The lights you will load must be of the same format as the flat files. The result will be stored in this way:

  • if a .jpg is processed, then the result will be stored also in .jpg format
  • if a .tif is processed, then the result will be stored also in .tif format
  • if a raw file (either .nef or .cr2) is processed, then the result will be stored in .tif format

Processing of images is done in two ways:

  • rgb channels are processed witout separation of channels.
  • rgb channels are processed separately. Depending on the input images once the method separated channels or the method without separation will give the better correction

At the end of the program a preview of the corrected image is given in comparison with the uncorrected, original image for both methods. The corrected images are stored in the same directory as the light images. They are named ‚original-filename_cor_cs‘ in case of rgb channel separation or ‚original-filename_cor_nocs‘ in the case of no rgb channel separation.

Example:

  1. Picture of  thallus section of Peltigera leucophlebia as being shot,
  2. the corresponding flat image
  3. and the corrected image:

              1                                              2                                        3

Download: download yafft

 

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