XYT Bleach Correction

FIJI Macro for performing xyt bleach correction using the histogram matching method (https://imagej.net/Bleach_Correction) 
and file conversion to be opened in Imaris. Inspired by users on BIDC's Zeiss Widefield microscope.

  • FIJI BleachCorrection plugin  
  • FIJI BioFormats 
  • Download at GitHub.
  • Create a folder for input images and one for resultant output images. 
  • Open your image stack in FIJI. 
  • In FIJI  
    • Plugins > Macros > Run... 
    • Select the text file named wideguy_xyt_bleachcorrect_Imaris.txt  
  • Choose input folder. 
  • Choose output folder. 
  • From the popup window select which channels you wish to perform the bleach correction on.
  • Grab coffee. 
  • .ics and .ids file for each image stack. 
  • To open the output in Imaris, drag the .ics file into Imaris' Surpass.  
  • Intended only for use of 2-channel time-series from Manager output files. 
  • Does not work for z-stacks...yet.