Project 3 grayscale images into a single RGB image, as done with "stack to RGB" in ImageJ

So, I have three different tiff stacks that are gray scale. I loop through each image of each stack, concatenating them together. I then want to something like "Stack to RGB in ImageJ, where these three grayscale images are converted into a single image that's color-coded according the the similarity between the three images. Ultimately, I will be writing a tiff stack that has the same number of frames as each of the three original grayscale tiff stacks, but colored to show differences in an animal's behavior across three conditions. My approach is below, showing how I loop through the number of frames in the tiff stacks, concatenate, and then attempt to write the RGB image.

for frame = 1:num_frames

if frame == 1 && exist([video_dir '\Peristim_RGB_mov.tif'])

display('Peristim_RGB_mov already exists. Delete in order to proceed.');

end

    grey = [];

    grey = cat(3,grey,imread([video_dir '\CS_shock_MovMean'],'tif',frame));

    grey = cat(3,grey,imread([video_dir '\CS_neutral_MovMean'],'tif',frame));

    grey = cat(3,grey,imread([video_dir '\CS_food_MovMean'],'tif',frame));

    %rgb  = repmat(double(grey)./255,1);

    RGB_frame = mean(rgb,3);

    try

        imwrite(RGB_frame,'Peristim_RGB_mov.tif','WriteMode','append', ...

            'Compression','none');

    catch err

        pause(0.1);

        imwrite(RGB_frame,'Peristim_RGB_mov.tif','WriteMode','append', ...

            'Compression','none');

    end

end

[Image Analyst]

What is a "stack"? Is it some number of gray scale images? If so, how many? Is it some number of color images, like a multi-page Tiff image? If so, how many color images are in the stack? And after all is done, how many image planes will be in grey? 3? 9? More?

[Pavlov]

The three original "stacks" are 546 frame tiff movies. The final RGB movie will also be 546 frames, because each frame of the three originals will be smooshed into a single RGB image.

[Image Analyst]

546 grayscale frames, or color frames? When you say "each frame of the three originals will be smooshed into a single RGB image" do you mean that each frame the 3 movies is a gray scale image that supposed to be one color channel of the output frame, so it takes one frame from each stack to create one frame of the RGB output movie?

[Pavlov]

Yes, 546 grayscale frames. I am looping through each frame for each of the three tiff stacks, concatenating, then trying to convert to single RGB frame so that the final movie is also 546 frames. The idea is to do something equivalent to "Stack to RGB" in ImageJ. So, for example, if you take frame #1 for each of the three grayscale movies, you concatenate, then convert to a single RGB image such that MOre red colors signify areas of teh image unique to the first grayscale frame of the three, more green for the second, and more blue for the third.

Answer 1

[Pavlov]

Haven't thought about this since last week, but will attempt to make it work again this afternoon. Any ideas?

Answer 2

[Image Analyst]

Read in images 1-3, concatenate them into an rgb image, and make a video frame. Then read in images 2-4 and do the same thing, then images 3-5, etc. Attached is a demo for how to create a movie from individual RGB images.