NeutralKaon/do_Over​lay

Overlay one greyscale image in colour atop another, e.g. for medical imaging, simply.

Often, one wants to overlay one image on top of another in Matlab. This is inevitably needlessly difficult. do_Overlay is a script that takes at a minimum two arguments: im_underlay, and im_overlay. These have to have the same in-plane size (i.e. size(im_underlay,1)==size(im_overlay,1); size(im_underlay,2)==size(im_overlay,2)). The result is a colour image of overlay superimposed on underlay, with scalings, opacities, etc dealt with appropriately according to your colormap of choice.
The overlay (colour) image can have a third dimension, which is assumed to be 'time'. A movie would then be made (with pause statements between each frame to allow for slow video writing). The colour axis is normalised to the max over all time. This is typically used for producing movies of, e.g. contrast agents flashing through a medical imaging reference scan.

Options are parsed as a struct with a set of sensible defaults, and can contain:
hfig -- figure handle for overlay window
hax -- axis handle (blank is fine)
do_normslice = 1 -- normalise each slice
orient =1 -- change to rotate
overlay_flag = 'abs' -- function to call on overlayed data
cmap = 'jet' -- overlay colour scheme
bgnd_bright = 0.6 -- brightness of the background [underlay]
gamma_background = 0.5 -- gamma adjustment of the background
fov_x = 1 -- adjust to crop
fov_y = 1 -- adjust to crop
zoomFactor = 1.5 -- size of resulting window
cutBottom = 0.45 -- bottom of the colour axis (below which is
transparent)
cutTop = 1 -- top of the colour axis (above which is red)
saveVideo = false -- set to true to save a video
videoName = a unique string -- filename
overlayString -- text to write on each video frame
An example (with somewhat pointless data from the image processing toolbox):

underlay = imread('cameraman.tif'); %256x256 greyscale image of a man with a camera
overlay = imread('circles.png'); %256x256 binary image of circles
overlay = imfilter(double(overlay),fspecial('gaussian',8,20)); %Blur circles
do_Overlay(underlay, overlay);
%256x256 RGB image of a man with a camera in B&W with an overlaid set of discs: