diff --git a/Data-Analyzer/+Analyzer/conductPCA.m b/Data-Analyzer/+Analyzer/conductPCA.m
index cb6dd2f..1b2516e 100644
--- a/Data-Analyzer/+Analyzer/conductPCA.m
+++ b/Data-Analyzer/+Analyzer/conductPCA.m
@@ -106,6 +106,6 @@ function conductPCA(od_imgs, scan_reference_values, scan_parameter_values, doPlo
     
     %% --- ANOVA Test ---
     p = anova1(score(:,1), arrayfun(@num2str, scan_parameter_values, 'UniformOutput', false), 'off');
-    fprintf('ANOVA p-value for PC1 score differences between groups: %.4e\n', p);
+    fprintf('[INFO] ANOVA p-value for PC1 score differences between groups: %.4e\n', p);
 
 end
diff --git a/Data-Analyzer/+Analyzer/performAnalysis.m b/Data-Analyzer/+Analyzer/performAnalysis.m
index 74d5473..dd634ad 100644
--- a/Data-Analyzer/+Analyzer/performAnalysis.m
+++ b/Data-Analyzer/+Analyzer/performAnalysis.m
@@ -47,7 +47,7 @@ function [results, scan_parameter_values] = performAnalysis(options)
     [od_imgs, scan_parameter_values, ~] = Helper.collectODImages(options);
 
     % Conduct spectral analysis
-    fprintf('\nInitiating spectral analysis...\n');
+    fprintf('\n[INFO] Initiating spectral analysis...\n');
     
     spectral_analysis_results        = Analyzer.conductSpectralAnalysis(od_imgs, scan_parameter_values, options);
     
@@ -63,7 +63,7 @@ function [results, scan_parameter_values] = performAnalysis(options)
                                         spectral_analysis_results.angular_spectral_distribution, ...
                                         scan_parameter_values, N_shots, options.N_angular_bins);
     
-    fprintf('\nSpectral analysis complete!\n');
+    fprintf('\n[INFO] Spectral analysis complete!\n');
 
     % PCA
 
diff --git a/Data-Analyzer/+Helper/batchAnalyze.m b/Data-Analyzer/+Helper/batchAnalyze.m
index 4e9b692..3ae4f91 100644
--- a/Data-Analyzer/+Helper/batchAnalyze.m
+++ b/Data-Analyzer/+Helper/batchAnalyze.m
@@ -8,6 +8,9 @@ function results_all = batchAnalyze(dataSources, options)
     if ~isfield(options, 'baseDataFolder')
         options.baseDataFolder = '//DyLabNAS/Data';
     end
+    
+    % ===== Estimate dataset memory and get per-run estimates =====
+    [options.SAVE_TO_WORKSPACE, runMemoryGB] = estimateDatasetMemory(dataSources, options);
 
     results_all = {};  % one element per folder
 
@@ -37,6 +40,13 @@ function results_all = batchAnalyze(dataSources, options)
                 error('Unsupported type for run entry: %s', class(runItem));
             end
 
+            % --- Check per-run memory before processing ---
+            if runMemoryGB(j) > 0.5 * getAvailableRAM()
+                fprintf('[WARNING] Skipping run %s/%s due to high memory requirement (%.2f GB)\n', ...
+                        ds.sequence, runID, runMemoryGB(j));
+                continue; % skip this run
+            end
+
             % Build folder path
             folderPath         = fullfile(baseFolder, runID);
             options.folderPath = folderPath;
@@ -75,7 +85,6 @@ function results_all = batchAnalyze(dataSources, options)
     end
 end
 
-
 %% ---- Local function for saving results ----
 function saveResultStruct(result, saveDirectory)
     % Define results folder
@@ -107,3 +116,13 @@ function saveResultStruct(result, saveDirectory)
     nextIdx = nextIdx + 1;
     save(indexFile, "nextIdx");
 end
+
+%% ---- Local function to get available RAM ----
+function availableRAM = getAvailableRAM()
+    if ispc
+        [~, sys] = memory;
+        availableRAM = sys.PhysicalMemory.Available;
+    else
+        availableRAM = 16e9; % fallback: 16 GB if not Windows
+    end
+end
diff --git a/Data-Analyzer/+Helper/collectODImages.m b/Data-Analyzer/+Helper/collectODImages.m
index d4a3c4e..baed8ca 100644
--- a/Data-Analyzer/+Helper/collectODImages.m
+++ b/Data-Analyzer/+Helper/collectODImages.m
@@ -25,6 +25,12 @@ function [od_imgs, scan_parameter_values, file_list] = collectODImages(options)
     reuseVarsExist = evalin('base', ...
         'exist(''od_imgs'',''var'') && exist(''scan_parameter_values'',''var'') && exist(''file_list'',''var'') && exist(''prior_options'',''var'')');
 
+    % --- Respect SAVE_TO_WORKSPACE flag from batchAnalyze ---
+    if isfield(options, 'SAVE_TO_WORKSPACE') && ~options.SAVE_TO_WORKSPACE
+        % Force reprocessing: skip all workspace reuse
+        reuseVarsExist = false;
+    end
+
     if reuseVarsExist
         prior_options = evalin('base','prior_options');
 
@@ -32,7 +38,7 @@ function [od_imgs, scan_parameter_values, file_list] = collectODImages(options)
         critical_fields = {'folderPath','cam','angle','ImagingMode','PulseDuration','center','span','fraction','removeFringes','skipUnshuffling','scan_reference_values'};
 
         if ~haveOptionsChanged(options, prior_options, critical_fields)
-            fprintf('\nReusing processed OD images, scan parameters, and file list from memory.\n');
+            fprintf('\n[INFO] Reusing processed OD images, scan parameters, and file list from memory.\n');
             od_imgs               = evalin('base','od_imgs');
             scan_parameter_values = evalin('base','scan_parameter_values');
             file_list             = evalin('base','file_list');
@@ -44,7 +50,7 @@ function [od_imgs, scan_parameter_values, file_list] = collectODImages(options)
 
             return; % ✅ safe to exit now
         else
-            fprintf('\nProcessed-data-related options changed. Reprocessing full OD image dataset...\n');
+            fprintf('\n[INFO] Processed-data-related options changed. Reprocessing full OD image dataset...\n');
         end
     end
 
@@ -55,6 +61,11 @@ function [od_imgs, scan_parameter_values, file_list] = collectODImages(options)
                      evalin('base', 'exist(''raw_file_list'', ''var'')') && ...
                      evalin('base', 'exist(''prior_options'',''var'')');
 
+    % --- Respect SAVE_TO_WORKSPACE flag ---
+    if isfield(options, 'SAVE_TO_WORKSPACE') && ~options.SAVE_TO_WORKSPACE
+        fullDataExists = false;  % force recompute even if workspace vars exist
+    end
+
     if fullDataExists
         % Both required datasets exist, check if raw-data options changed
         prior_options = evalin('base','prior_options');
@@ -63,36 +74,40 @@ function [od_imgs, scan_parameter_values, file_list] = collectODImages(options)
         critical_raw_fields = {'folderPath','cam','angle','ImagingMode','PulseDuration'};
 
         if ~haveOptionsChanged(options, prior_options, critical_raw_fields)
-            fprintf('\nReusing full OD image dataset and scan parameters from memory.\n');
+            fprintf('\n[INFO] Reusing full OD image dataset and scan parameters from memory.\n');
             full_od_imgs              = evalin('base', 'full_od_imgs');
             full_bkg_imgs             = evalin('base', 'full_bkg_imgs');
             raw_scan_parameter_values = evalin('base', 'raw_scan_parameter_values');
             raw_file_list             = evalin('base', 'raw_file_list');
         else
-            fprintf('\nRaw-data-related options changed. Recomputing full OD image dataset...\n');
+            fprintf('\n[INFO] Raw-data-related options changed. Recomputing full OD image dataset...\n');
             [full_od_imgs, full_bkg_imgs, raw_scan_parameter_values, raw_file_list] = Helper.processRawData(options);
 
             % Save raw full dataset for reuse
+            if options.SAVE_TO_WORKSPACE
+                assignin('base', 'full_od_imgs', full_od_imgs);
+                assignin('base', 'full_bkg_imgs', full_bkg_imgs);
+                assignin('base', 'raw_scan_parameter_values', raw_scan_parameter_values);
+                assignin('base', 'raw_file_list', raw_file_list);
+            end
+            fprintf('\n[INFO] Completed recomputing OD images. Stored in workspace for reuse.\n');
+        end
+    else
+        % Either dataset is missing, process raw HDF5 files completely
+        fprintf('\n[INFO] Full OD image dataset or scan parameters not found in memory.\n');
+        [full_od_imgs, full_bkg_imgs, raw_scan_parameter_values, raw_file_list] = Helper.processRawData(options);
+
+        % Save raw full dataset for reuse
+        if options.SAVE_TO_WORKSPACE
             assignin('base', 'full_od_imgs', full_od_imgs);
             assignin('base', 'full_bkg_imgs', full_bkg_imgs);
             assignin('base', 'raw_scan_parameter_values', raw_scan_parameter_values);
             assignin('base', 'raw_file_list', raw_file_list);
-            fprintf('\nCompleted recomputing OD images. Stored in workspace for reuse.\n');
         end
-    else
-        % Either dataset is missing, process raw HDF5 files completely
-        fprintf('\nFull OD image dataset or scan parameters not found in memory.\n');
-        [full_od_imgs, full_bkg_imgs, raw_scan_parameter_values, raw_file_list] = Helper.processRawData(options);
-
-        % Save raw full dataset for reuse
-        assignin('base', 'full_od_imgs', full_od_imgs);
-        assignin('base', 'full_bkg_imgs', full_bkg_imgs);
-        assignin('base', 'raw_scan_parameter_values', raw_scan_parameter_values);
-        assignin('base', 'raw_file_list', raw_file_list);
-        fprintf('\nCompleted computing OD images. Images will be stored in workspace for reuse.\n');
+        fprintf('\n[INFO] Completed computing OD images. Images will be stored in workspace for reuse.\n');
     end
     
-    fprintf('\nCropping and subtracting background from images...\n');
+    fprintf('\n[INFO] Cropping and subtracting background from images...\n');
     nFiles = size(full_od_imgs, 3);
     
     % --- Preallocate arrays for processed images ---
@@ -144,18 +159,18 @@ function [od_imgs, scan_parameter_values, file_list] = collectODImages(options)
 
     % --- Optional fringe removal ---
     if isfield(options, 'removeFringes') && options.removeFringes
-        fprintf('\nApplying fringe removal to processed images...\n');
+        fprintf('\n[INFO] Applying fringe removal to processed images...\n');
         optrefimages             = Helper.removeFringesInImage(absimages, refimages);
         absimages_fringe_removed = absimages - optrefimages;
         od_imgs                  = arrayfun(@(i) absimages_fringe_removed(:,:,i), 1:nFiles, 'UniformOutput', false);
-        fprintf('\nFringe removal completed.\n');
+        fprintf('\n[INFO] Fringe removal completed.\n');
     else
         od_imgs                  = arrayfun(@(i) absimages(:,:,i), 1:nFiles, 'UniformOutput', false);
     end
 
     % --- Optional unshuffling based on scan reference values ---
     if isfield(options, 'skipUnshuffling') && ~options.skipUnshuffling
-        fprintf('\nReordering images according to scan parameter reference values...\n');
+        fprintf('\n[INFO] Reordering images according to scan parameter reference values...\n');
 
         n_values = length(options.scan_reference_values);
         n_total  = length(raw_scan_parameter_values);
@@ -186,7 +201,7 @@ function [od_imgs, scan_parameter_values, file_list] = collectODImages(options)
         od_imgs                       = ordered_od_imgs;
         scan_parameter_values         = ordered_scan_parameter_values;
         file_list                     = ordered_file_list;
-        fprintf('\nImage reordering completed.\n');
+        fprintf('\n[INFO] Image reordering completed.\n');
     else
         % No unshuffling: keep original order
         scan_parameter_values         = raw_scan_parameter_values;
@@ -204,7 +219,7 @@ function [od_imgs, scan_parameter_values, file_list] = collectODImages(options)
         saveODFigures(od_imgs, options.saveDirectory);
     end
 
-    fprintf('\nOD image dataset ready for further analysis.\n');
+    fprintf('\n[INFO] OD image dataset ready for further analysis.\n');
 
 end
 
@@ -234,11 +249,11 @@ function saveODFigures(od_imgs, saveDirectory)
     filesExist = all(arrayfun(@(k) isfile(fullfile(odFolder, sprintf('OD_img_%03d.fig', k))), 1:nImgs));
 
     if filesExist
-        fprintf('\nOD figures already exist in %s. Skipping save.\n', odFolder);
+        fprintf('\n[INFO] OD figures already exist in %s. Skipping save.\n', odFolder);
         return;
     end
 
-    fprintf('\nSaving OD figures to %s ...\n', odFolder);
+    fprintf('\n[INFO] Saving OD figures to %s ...\n', odFolder);
     for k = 1:nImgs
         img = od_imgs{k};
 
@@ -252,5 +267,5 @@ function saveODFigures(od_imgs, saveDirectory)
         savefig(hFig, fileName);
         close(hFig);
     end
-    fprintf('OD figures saved successfully.\n');
+    fprintf('[INFO] OD figures saved successfully.\n');
 end
diff --git a/Data-Analyzer/+Helper/estimateDatasetMemory.m b/Data-Analyzer/+Helper/estimateDatasetMemory.m
new file mode 100644
index 0000000..086ab9b
--- /dev/null
+++ b/Data-Analyzer/+Helper/estimateDatasetMemory.m
@@ -0,0 +1,70 @@
+function [SAVE_TO_WORKSPACE, runMemoryGB] = estimateDatasetMemory(dataSources, options)
+% Estimate per-run memory and decide whether to save dataset to workspace
+
+    % --- Measured memory per image (bytes) ---
+    bytesPerFullImage    = 37.75 * 1e6;  % full OD image
+    bytesPerCroppedImage = 0.16  * 1e6;  % cropped OD image
+
+    % --- Check available RAM on Windows ---
+    if ispc
+        [~, sys] = memory;
+        availableRAM = sys.PhysicalMemory.Available;
+    else
+        availableRAM = 16e9; % fallback: 16 GB if not Windows
+    end
+
+    SAVE_TO_WORKSPACE = true; % default, may change per run
+    runMemoryGB = [];         % store per-run memory
+
+    % --- Loop over all data sources and runs ---
+    for i_ds = 1:numel(dataSources)
+        ds = dataSources{i_ds};
+
+        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_run = 1:numel(ds.runs)
+            runItem = ds.runs(j_run);
+
+            % Convert runItem to string runID
+            if isnumeric(runItem)
+                runID = sprintf('%04d', runItem);
+            elseif isstring(runItem)
+                runID = runItem;
+            elseif ischar(runItem)
+                runID = string(runItem);
+            elseif iscell(runItem)
+                runID = string(runItem{1});
+            else
+                error('Unsupported run type');
+            end
+
+            runFolder = fullfile(baseFolder, runID);
+
+            if isfolder(runFolder)
+                files = dir(fullfile(runFolder, '*.h5'));
+                nFiles = numel(files);
+                if nFiles == 0
+                    continue;
+                end
+
+                % Memory estimate for this run (full + cropped)
+                runBytes = nFiles * (bytesPerFullImage + bytesPerCroppedImage);
+                runMemoryGB(end+1,1) = runBytes/1e9;
+
+                % Decide workspace flag per run by comparing with 50% of available RAM
+                if runBytes > 0.5 * availableRAM
+                    SAVE_TO_WORKSPACE = false;
+                    fprintf('[INFO] Estimated size on memory of Run %s/%s too large (%.2f GB). Not saving to workspace.\n', ...
+                        ds.sequence, runID, runBytes/1e9);
+                else
+                    fprintf('[INFO] Estimated size on memory of Run %s/%s = %.2f GB. Will save to workspace.\n', ...
+                        ds.sequence, runID, runBytes/1e9);
+                end
+            end
+        end
+    end
+end
\ No newline at end of file
diff --git a/Data-Analyzer/+Helper/processRawData.m b/Data-Analyzer/+Helper/processRawData.m
index dd6d3b6..04310d3 100644
--- a/Data-Analyzer/+Helper/processRawData.m
+++ b/Data-Analyzer/+Helper/processRawData.m
@@ -6,7 +6,7 @@ function [full_od_imgs, full_bkg_imgs, raw_scan_parameter_values, raw_file_list]
 % Returns the OD images and scan parameters immediately in memory.
 % This function does NOT do cropping or fringe removal.
 
-    fprintf('\nProcessing raw data files at %s ...\n', options.folderPath);
+    fprintf('\n[INFO] Processing raw data files at %s ...\n', options.folderPath);
     
     % ===== Group paths in HDF5 files =====
     groupList = ["/images/MOT_3D_Camera/in_situ_absorption", ...