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README.txt
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README.txt
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// Name:
// wideguy_xyt_bleachcorrect_Imaris_v2.txt
//
// Description:
// 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 BIDC's
// wideguy microscope, Ed Roberts and Kelly Kersten
//
// Usage:
// 0) Create a folder for input images and one for resultant output images
// 1) Open your image stack in FIJI
// 2) In FIJI:
// Plugins -> Macros -> Run...
// and select the text file named wideguy_xyt_bleachcorrect_Imaris.txt
// 3) Choose the input folder
// 4) Choose the output folder
// 5) From the popup window select which channels you wish to perform the bleach correction
// 5) Grab coffee
//
// Output:
// .ics and .ids file for each image stack
//
// to open the output in Imaris, drag the .ics file into Imaris' Surpass
//
// Author:
// Adam Fries 2018.02.21
//
// Details:
// Intended only for use of 2-channel time-series from uManager output files
// Does not work for z-stacks...yet
//
// Dependencies:
// FIJI BleachCorrection plugin
// FIJI BioFormats