A set of scripts to manipulate Zeiss CZI options in Bio-Formats

open_czi.m

% Check Bio-Formats and initialize logging
bfCheckJavaPath();
bfInitLogging();

% Create a reader
r =  bfGetReader();

values = [true false];
for autostich = values
    for attachments = values 
        % Create a set of key/value options and pass it to the reader
        m = loci.formats.in.DynamicMetadataOptions();
        m.setBoolean(loci.formats.in.ZeissCZIReader.ALLOW_AUTOSTITCHING_KEY,...
            java.lang.Boolean(autostich));
        m.setBoolean(loci.formats.in.ZeissCZIReader.INCLUDE_ATTACHMENTS_KEY,...
            java.lang.Boolean(attachments));
        r.setMetadataOptions(m);
        
        for flattenedResolutions = values
            r.setFlattenedResolutions(flattenedResolutions);
            % Initialize the reader with the file
            r.setId(path_to_czi);
            
            % Display metadata
            fprintf(1, 'Autostitch: %g\n', autostich);
            fprintf(1, 'Include attachments: %g\n', attachments);
            fprintf(1, 'Flatten resolutions: %g\n', flattenedResolutions);
            fprintf(1, 'Number of series: %g\n', r.getSeriesCount());
            fprintf(1, 'Number of resolutions: %g\n', r.getResolutionCount());
            fprintf(1, '\n');
            % Close the reader
            r.close();
        end
    end
end

open_czi.txt

// A macro derived from basicMetadata to set the CZI arguments

// Set option to disable auto-stitching and attachments
call("ij.Prefs.set", "bioformats.zeissczi.allow.autostitch", "false");
call("ij.Prefs.set", "bioformats.zeissczi.include.attachments", "false");

run("Bio-Formats Macro Extensions");

id = File.openDialog("Choose a file");
Ext.setId(id);
Ext.getSeriesCount(seriesCount);
for (s=0; s<seriesCount; s++) {
  Ext.setSeries(s);
  Ext.getSizeX(sizeX);
  Ext.getSizeY(sizeY);
  Ext.getSizeZ(sizeZ);
  Ext.getSizeC(sizeC);
  Ext.getSizeT(sizeT);
  print("Series #" + s + ": image resolution is " + sizeX + " x " + sizeY);
  print("Focal plane count = " + sizeZ);
  print("Channel count = " + sizeC);
  print("Time point count = " + sizeT);
}
Ext.close();

Both the scripts work. The only thing that I might like to add to the matlab script is a loop like the Fiji example, to print the series count etc. Then it would become a self-sufficient example and potentially a base script for a unit-test in future.

Thanks @bramalingam, done in 3c9f27de36339b5f2ae03b21599b20d2 and added the flattened resolutions call.