Overlaid images: more than one axis in a subplot?

I need to subplot two images that are overlaid. I only managed to overlay them using two axis for the same figure (note that both fifgures have it's own colormap). But now I need to subplot 6 pairs of overlaid images... I can't find the way of subplotting two axis in a subplot.

I need to overlaid some pixels of a a color image (activation level) over a background in black and white. This is what I did to overlaid:

Cmap =  data.activmap(:,:,600,20); % image of activation to plot 
backgr = data.backgr(:,:); %background image
backim= mat2gray(backgr); imshow(backim)

figure; % I need this one in a subplot (together with other similar)
ax1 = axes;
imagesc(backgr);
colormap(ax1,'bone');
ax2 = axes;
imagesc(ax2,Cmap,'alphadata',Cmap>0.02);
colormap(ax2,polarmap(jet));
caxis(ax2,[min(nonzeros(Cmap)) max(nonzeros(Cmap))]);
ax2.Visible = 'off';
linkprop([ax1 ax2],'Position');
colorbar;

I have unsuccessfully tried some alternatives.. could anyone give me a hand? (thanks)

[Akira Agata]

How about using yyaxis in subplot?

[Tamara del Águila]

Interesting... but how could I implement it with images?

(thanks for answering)

Answer 1

[Tamara del Águila]

Right after asking, I came up myself with one solution... (had I known I would have asked before!).

What I did was a function in which I pass the subplot axis handle as an input, and then inside the function I align them all respect to the input axis handle...

If anyone knows a better solution, I'll be pleased to listen to it!

Cmap =  VSDmoviep10.data(:,:,600,20); %colorimage (to overlaid pixels above threshold)
backgr = VSDI.backgr(:,:,1); % black&white background 
backim= mat2gray(backgr); 

% threshold above which to plot Cmap
thresh = 0.02 %

fig=figure;
ax1 = subplot(2,2,3);
plot_framesoverlaid(Cmap, backgr, thresh , ax1); 

And the function:

function plot_framesoverlaid(imAct, imBack, thresh, plotnow, axH)
% Overlay colormap over greyscale background
ax1 = axes;
imagesc(imBack);
colormap(ax1,'bone');
ax2 = axes;
imagesc(ax2,imAct,'alphadata',imAct>thresh);
colormap(ax2,polarmap(jet));
caxis(ax2,[min(nonzeros(imAct)) max(nonzeros(imAct))]);
ax2.Visible = 'off';
colorbar;
linkprop([axH ax1 ax2],'Position');
end

[Akira Agata]

Thank you for clarifying your question and providing your code. But, unfortunately, I couldn't run your code and came across some errors.

If possible, could you provide what the desired output looks like?

[Tamara del Águila]

Sure!

By the way, I just noticed that I forgot to remove the input 'plotnow' from that simplified version I posted before.

I also copy the final function I am working with at the end of the response. I have changed the input 'threshold' by an 'logicalpha' (transparency) matrix . And this is how it looks:

( I have not adapted the function to the case in which the handle is not provided, but can be easily done)

function  plot_framesoverlaid(imAct, imBack, logicalpha, plotnow, axH, act_clim, plot_cbar)
% Overlay an color image over a  background

% INPUT 
% 'imAct' - image to display in colors
% 'imBack' - background image
% 'logicalpha': logic matrix with transparency information (1 = shown pixel)
% 'plotnow': whether we want to plot the figure (set to 0 if we are providing a axisHandle)
% 'axH': axes handle in which to plot it, when it's going to be included into a subplot
% 'act_clim': color limits for 'imAct'. If no color limits is provided for the activity (color) map, use the max
% and min from the input movie
% 'plot_cbar' : whether we want to plot the colorbar (useful in subplots)


if ~exist('act_clim')
    act_clim = [min(nonzeros(imAct(:))) max(nonzeros(imAct(:)))];
elseif isempty(act_clim)
    act_clim = [min(nonzeros(imAct(:))) max(nonzeros(imAct(:)))];
end

if ~exist('thresh')
    thresh = 0;
elseif isempty(thresh)
        thresh = 0;
end

if ~exist('plotnow')
        plotnow= 1;
elseif isempty(plotnow)
        plotnow= 1;
end 

if ~exist('plot_cbar')
        plot_cbar= 1;
elseif isempty(plot_cbar)
        plot_cbar= 1;
end 

% end of input control ------------------------

if plotnow
    fig1 = figure; 
end

ax1 = axes;
imagesc(imBack);
colormap(ax1,'bone');
ax1.Visible = 'off';

ax2 = axes;
% imagesc(ax2,imAct,'alphadata',imAct>thresh);
imagesc(ax2,imAct,'alphadata',logicalpha);
colormap(ax2,polarmap(jet));
caxis(ax2, act_clim);
ax2.Visible = 'off';

if plot_cbar 
colorbar;
end
linkprop([axH ax1 ax2],'Position');

end