Pyramidal OME-TIFF using the Bio-Formats API

% Add the Bio-Formats toolbox to the MATLAB path
addpath('path_to_bfmatlab_folder');

% Import the necessary Bio-Formats classes
import loci.formats.*;

% Create a Bio-Formats Reader for your input images
reader = loci.formats.ChannelFiller();

% Configure metadata for the output pyramidal OME-TIFF
metadata = loci.formats.MetadataTools.createOMEXMLMetadata();

% Define the output file name
outputFile = 'output.ome.tif';

% Set the number of pyramid levels (e.g., 5 levels)
numPyramidLevels = 5;

% Load your input images (assuming you have them in an 'images' cell array)
images = cell(numPyramidLevels, 1);
for level = 1:numPyramidLevels
    % Load the image for the current level
    image = imread(['image_level_' num2str(level) '.tif']);

    % Store the image in the 'images' cell array
    images{level} = image;
end

% Write the pyramid levels to the output OME-TIFF
for level = 1:numPyramidLevels
    % Set the resolution level for the current image
    metadata.setPixelsSizeC(0, images{level}, level - 1);

    % Write the image to the Bio-Formats reader
    reader.setId(outputFile);
    reader.setSeries(0);
    reader.saveBytes(0, images{level}, level - 1);
end

% Close the Bio-Formats reader
reader.close();

% Save metadata to the output OME-TIFF
loci.formats.FileStitcher.writeOME(metadata, outputFile);