Import Nikon ND2 image files, extract metadata, register images, choose ROIs, and quantify fluorescence/FRET
This script takes as input ND2 files from a Ti-E widefield, spinning disk, or A1R laser scanning confocal microscope (it probably works on other ND2 files as well, but the metadata that it outputs may be incomplete)
The script allows you to define which channels you're looking at and whether you're looking at FRET. It registers all images, if able (and if unsuccessful, allows you to try to modify the input images so that it can register them). It then allows for ROI definition either by drawing rectangles or matrix input. This script does NOT automatically segment anything, or allow for non-rectangular ROIs. It does intensity measurements and background correction on all ROIs, then calculates ratios if the data is FRET. It outputs plots for background intensity (if desired), background-corrected ROI intensity of all channels, and FRET ratio (if applicable). It also outputs an image with associated ROIs, as well as all of the input data in a format which can be spit back into the script for later repeated analysis.
Z-stacks aren't really meant to work with this script. They might not break it if you only open one file that is not also a timecourse, but don't count on it.
IMPORTANT: If inputting multiple files into this script, they MUST have the same number/order of channels, otherwise it will be very broken.
IMPORTANT: This script only works with MATLAB R2016b and later, as local functions are not supported in earlier versions. You also must have downloaded the package 'bfmatlab' - go to http://downloads.openmicroscopy.org/bio-formats/ and choose the most recent version, then go into the 'artifacts' folder and download the 'bfmatlab.zip' folder. Extract this folder, then move it into your MATLAB toolbox folder (wherever your MATLAB is installed, this should be under 'MATLAB/version#/toolbox/'). Make sure this folder is also added to the MATLAB path.