function results_all = batchAnalyze(dataSources, options)
    arguments
        dataSources (1,:) cell
        options struct
    end

    % Default base folder if not specified
    if ~isfield(options, 'baseDataFolder')
        options.baseDataFolder = '//DyLabNAS/Data';
    end

    results_all = {};  % one element per folder

    for i = 1:numel(dataSources)
        ds = dataSources{i};

        % Use per-sequence baseFolder if present, otherwise default from options
        if isfield(ds, 'baseFolder') && ~isempty(ds.baseFolder)
            baseFolder = fullfile(ds.baseFolder, ds.sequence, ds.date);
        else
            baseFolder = fullfile(options.baseDataFolder, ds.sequence, ds.date);
        end

        for j = 1:numel(ds.runs)
            runItem = ds.runs(j);

            % Convert numeric or char arrays to a string with leading zeros if needed
            if isnumeric(runItem)
                runID = sprintf('%04d', runItem);  % adjust padding as needed
            elseif isstring(runItem)
                runID = runItem;
            elseif ischar(runItem)
                runID = string(runItem);
            elseif iscell(runItem)
                runID = string(runItem{1});  % handles cell of char
            else
                error('Unsupported type for run entry: %s', class(runItem));
            end

            % Build folder path
            folderPath         = fullfile(baseFolder, runID);
            options.folderPath = folderPath;
            
            try
                % Convert struct -> name-value args
                args = [fieldnames(options), struct2cell(options)]';
                args = args(:)';

                % Perform analysis
                analysisResults = Analyzer.performAnalysis(args{:});

                % Store flat struct with metadata + results
                result = struct();
                result.sequence = ds.sequence;
                result.date     = ds.date;
                result.run      = runID;
                result.path     = folderPath;
                result.results  = analysisResults;
                
                % Save each dataset as its own MAT file
                if ~isfield(options, 'skipSaveData') || ~options.skipSaveData
                    saveResultStruct(result, options.saveDirectory);
                end
                
                % Append to output
                results_all{end+1,1} = result;

            catch ME
                warning("Error processing %s/%s/%s: %s", ...
                        ds.sequence, ds.date, runID, ME.message);
            end
        end
    end
end

%% ---- Local function for saving results ----
function saveResultStruct(result, saveDirectory)
    % Define results folder
    resultsFolder = fullfile(saveDirectory, "Results", "AnalysisSavedData");
    if ~exist(resultsFolder, 'dir')
        mkdir(resultsFolder);
    end

    % Path to index file
    indexFile = fullfile(resultsFolder, "datasetsIndex.mat");

    % Load or initialize index
    if isfile(indexFile)
        S = load(indexFile, "nextIdx");
        nextIdx = S.nextIdx;
    else
        nextIdx = 1;
    end

    % Variable name and file path
    varName = sprintf('Dataset_%d', nextIdx);
    savePath = fullfile(resultsFolder, varName + ".mat");

    % Save dataset as struct inside MAT file
    S.(varName) = result;
    save(savePath, '-struct', 'S');

    % Update index
    nextIdx = nextIdx + 1;
    save(indexFile, "nextIdx");
end