diff --git a/BIOP_Clustering.m b/BIOP_Clustering.m
index 8e535c4..178d1b7 100644
--- a/BIOP_Clustering.m
+++ b/BIOP_Clustering.m
@@ -1,758 +1,784 @@
 function BIOP_Clustering
 %Start EasyXT
 addpath('EasyXT');
 addpath('functions');
 global X;
 X = EasyXT();
 
 f = figure('Name', 'BIOP - Clustering', ...
     'NumberTitle', 'off', 'Visible', 'off', 'Position', [0 0 700 512], ...
     'Tag', 'clustetring_main_f', ...
     'DockControls', 'off', 'ToolBar', 'none', 'MenuBar', 'none');
 
 % Move the window to the center of the screen.
 movegui(f,'center');
 
 % Make the window visible.
 f.Visible = 'on';
 
 % Add 1 panel on the left and one on the right
 settingsp = uipanel(f,'Title','Settings', 'Tag', 'p_settings',...
     'Position',[.05 .05 .65 .9]);
 
 commandsp = uipanel(f,'Title','Actions', 'Tag', 'p_commands',...
     'Position',[.70 .05 .25 .9]);
 
 % Settings Tab
 uitabgroup('Parent', settingsp, 'Tag', 'tab_channels');
 
 % Add buttons for refreshing data, and batch
 h = .1;
 w = .9;
 l = .05;
 
 uicontrol(commandsp,'Style','pushbutton','String','Refresh',...
     'Units','normalized', 'Tag', 'btn_refresh', ...
     'Position',[l .90 w h],...
     'Callback', @btn_refresh_callback);
 uicontrol(commandsp,'Style','pushbutton','String','Get Sum Channel',...
     'Units','normalized', 'Tag', 'btn_sum', ...
     'Position',[l .8 w h],...
     'Callback', @btn_sum_callback);
 uicontrol(commandsp,'Style','pushbutton','String','Clear Outside Sum Channel',...
     'Units','normalized', 'Tag', 'btn_clear_outside', ...
     'Position',[l .7 w h],...
     'Callback', @btn_clear_outside_callback);
 
 uicontrol(commandsp,'Style','pushbutton','String','Detect Spots',...
     'Units','normalized', 'Tag', 'btn_detect_spots', ...
     'Position',[l .6 w h],...
     'Callback', @btn_detect_spots_callback);
 
 uicontrol(commandsp,'Style','pushbutton','String','Cluster Spots',...
     'Units','normalized', 'Tag', 'btn_cluster_spots', ...
     'Position',[l .5 w h],...
     'Callback', @btn_cluster_spots_callback);
 
 uicontrol(commandsp,'Style','pushbutton','String','Reassign Spots',...
     'Units','normalized', 'Tag', 'btn_reassign_spots', ...
     'Position',[l .4 w h],...
     'Callback', @btn_reassign_spots_callback);
 
 % Load WingJ
 uicontrol(commandsp,'Style','pushbutton','String','Load WingJ Data',...
     'Units','normalized', 'Tag', 'btn_wingj', ...
     'Position',[l .3 w h],...
     'Callback', @btn_wingj_callback);
 
 uicontrol(commandsp,'Style','pushbutton','String','Export To CSV',...
     'Units','normalized', 'Tag', 'btn_export', ...
     'Position',[l .2 w h],...
     'Callback', @btn_export_callback);
 
 uicontrol(commandsp,'Style','text',...
     'String','Settings',...
     'Units','Normalized', ...
     'HorizontalAlignment', 'center', ...
     'Position',[l .10 w 0.05]);
 
 uicontrol(commandsp,'Style','pushbutton','String','Save',...
     'Units','normalized', 'Tag', 'btn_save', ...
     'Position',[l .05 w/2 h/2],...
     'Callback', @savebtn_callback);
 
 uicontrol(commandsp,'Style','pushbutton','String','load',...
     'Units','normalized', 'Tag', 'btn_load', ...
     'Position',[l+w/2 .05 w/2 h/2],...
     'Callback', @loadbtn_callback);
 
 % Make all the settings
 % Settings Tab
 tgroup = uitabgroup('Parent', settingsp, 'Tag', 'tab_channels');
 
 makeChanSumTab(tgroup);
 makeCleanChanTab(tgroup);
 makeSpotDetectionTab(tgroup);
 makeClusteringTab(tgroup);
 makeReassignTab(tgroup);
 makeWingJTab(tgroup)
 %makeExportTab(tgroup);
 
 end
 
 function makeChanSumTab(parent)
 global X;
 tabTag = 'tab_chan_sum';
 tabName = 'Sum Channels';
 thisTab = findobj('Tag',tabTag);
 if isempty(thisTab)
     thisTab = uitab('Parent', parent, 'Title', tabName, ...
         'Tag', tabTag);
     
     % Add all the controls
     %Control settings
     %Channels of interest as checkboxes
     sp = 0.05;
     nChan = X.GetSize('C');
     uicontrol(thisTab,'Style','text',...
         'String','Channels to Sum',...
         'Units','Normalized', ...
         'HorizontalAlignment', 'left', ...
         'Position',[.05 0.9 .3 sp]);
     
     for k=1:nChan;
         cbh(k) = uicontrol(thisTab, 'Style','checkbox','String',sprintf('Channel %d',k), ...
             'Tag', sprintf('is_sum_chan_%d',k), ...
             'Value',1, ...
             'Units', 'Normalized', ...
             'Position',[.05 .9-sp*k .3 sp]);
     end
     
     % Ask if we perform normalization
     uicontrol(thisTab, 'Style','checkbox','String','Normalize Channels Before Sum', ...
         'Tag', 'is_chan_norm', ...
         'Value',1, ...
         'Units', 'Normalized', ...
         'Position',[.05 0.9-sp*(nChan+3) .5 sp]);
     
 end
 end
 
 function makeCleanChanTab(parent)
 tabTag = 'tab_clean';
 tabName = 'Clean Channel';
 thisTab = findobj('Tag',tabTag);
 if isempty(thisTab)
     thisTab = uitab('Parent', parent, 'Title', tabName, ...
         'Tag', tabTag);
     
     % Add all the controls
     %Control position
     sp = 0.05;
     py = 0.89;
     
     % Channel for surface creation
     uicontrol(thisTab,'Style','text',...
         'String','Surface Channel',...
         'Units','Normalized', ...
         'HorizontalAlignment', 'right', ...
         'Position',[.05 py .3 sp]);
     
     uicontrol(thisTab,'Style','edit',...
         'String','',...
         'Units','Normalized', ...
         'Tag', 'txt_channel_surface', ...
         'Position',[.36 py+.01 .1 sp]);
     
     % Smoothing Factor for Surface
     uicontrol(thisTab,'Style','text',...
         'String','Surface Smoothing',...
         'Units','Normalized', ...
         'HorizontalAlignment', 'right', ...
         'Position',[.05 py-sp .3 sp]);
     
     uicontrol(thisTab,'Style','edit',...
         'String','5.0',...
         'Units','Normalized', ...
         'Tag', 'txt_surface_smooth', ...
         'Position',[.36 py+.01-sp .1 sp]);
     
     % Surface Intensity Threshold
     uicontrol(thisTab,'Style','text',...
         'String','Intensity Threshold',...
         'Units','Normalized', ...
         'HorizontalAlignment', 'right', ...
         'Position',[.05 py-2*sp .3 sp]);
     
     uicontrol(thisTab,'Style','edit',...
         'String','15',...
         'Units','Normalized', ...
         'Tag', 'txt_surface_intensity_threshold', ...
         'Position',[.36 py+.01-2*sp .1 sp]);
 end
 end
 
 function makeSpotDetectionTab(parent)
 tabTag = 'tab_detect';
 tabName = 'Detect Spots';
 thisTab = findobj('Tag',tabTag);
 if isempty(thisTab)
     thisTab = uitab('Parent', parent, 'Title', tabName, ...
         'Tag', tabTag);
     
     % Add all the controls
     %Control position
     sp = 0.05;
     py = 0.89;
     % Spot Detection Channel
     uicontrol(thisTab,'Style','text',...
         'String','Spot Channel',...
         'Units','Normalized', ...
         'HorizontalAlignment', 'right', ...
         'Position',[.05 py .3 sp]);
     
     uicontrol(thisTab,'Style','edit',...
         'String','',...
         'Units','Normalized', ...
         'Tag', 'txt_channel_spot', ...
         'Position',[.36 py+.01 .1 sp]);
     
     % Spot Spot Sizes
     uicontrol(thisTab,'Style','text',...
         'String','Spot Size [um]',...
         'Units','Normalized', ...
         'HorizontalAlignment', 'right', ...
         'Position',[.05 py-sp .3 sp]);
     % XY
     uicontrol(thisTab,'Style','edit',...
         'String','2.8',...
         'Units','Normalized', ...
         'Tag', 'txt_spot_size_xy', ...
         'Position',[.36 py+.01-sp .1 sp]);
     % Z (Optional)
     uicontrol(thisTab,'Style','edit',...
         'String','2.8',...
         'Units','Normalized', ...
         'Tag', 'txt_spot_size_z', ...
         'Position',[.47 py+.01-sp .1 sp]);
     
     % Spot Quality Threshold
     uicontrol(thisTab,'Style','text',...
         'String','Spot Quality Threshold',...
         'Units','Normalized', ...
         'HorizontalAlignment', 'right', ...
         'Position',[.05 py-2*sp .30 sp]);
     
     uicontrol(thisTab,'Style','edit',...
         'String','15',...
         'Units','Normalized', ...
         'Tag', 'txt_spot_quality_threshold', ...
         'Position',[.36 py+.01-2*sp .1 sp]);
     
     % Remove Spots Closer than
     uicontrol(thisTab,'Style','checkbox',...
         'String','Remove Spots if closer than',...
         'Tag', 'is_remove_spots', ...
         'Units','Normalized', ...
         'Position',[.05 py-3*sp .40 sp]);
     
     uicontrol(thisTab,'Style','edit',...
         'String','1.0',...
         'Units','Normalized', ...
         'Tag', 'txt_spot_proximity_threshold', ...
         'Position',[.45 py-3*sp .07 sp]);
     
     uicontrol(thisTab,'Style','text',...
         'String','um to image edge',...
         'Units','Normalized', ...
         'HorizontalAlignment', 'left', ...
         'Position',[.53 py-3*sp-.01 .30 sp]);
     
     
 end
 end
 
 function makeClusteringTab(parent)
 tabTag = 'tab_cluster';
 tabName = 'Cluster';
 thisTab = findobj('Tag',tabTag);
 if isempty(thisTab)
     thisTab = uitab('Parent', parent, 'Title', tabName, ...
         'Tag', tabTag);
     
     % Add all the controls
     % Need 3 tabs: Manual Clustering, Brute Force and KMeans
     clusMode = uitabgroup('Parent', thisTab, 'Tag', 'tab_cluster_modes');
     
     %Settings for clustering tab
     makeSettingsClusterTab(clusMode);
     
     % Manual Tab
     makeManualClusterTab(clusMode);
     
     % Brute Force
     makeBruteClusterTab(clusMode);
     
     % KMeans Tab
     makeKMeansClusterTab(clusMode);
 end
 end
 
 function makeManualClusterTab(parent)
 tabTag = 'tab_cluster_manual';
 tabName = 'Manual';
 thisTab = findobj('Tag',tabTag);
 sp = .05;
 py = .89;
 
 if isempty(thisTab)
     thisTab = uitab('Parent', parent, 'Title', tabName, ...
         'Tag', tabTag);
     
     uicontrol(thisTab,'Style','checkbox',...
         'String','Use Manual Clustering',...
         'Tag', 'is_do_manual', ...
         'Units','Normalized', ...
         'HorizontalAlignment', 'right', ...
         'Position',[.05 py+sp .4 sp]);
     
     
     uicontrol(thisTab,'Style','text',...
         'String','Number of Categories',...
         'Units','Normalized', ...
         'HorizontalAlignment', 'right', ...
         'Position',[.05 py-sp .3 sp]);
     
     uicontrol(thisTab,'Style','edit',...
         'String','2',...
         'Units','Normalized', ...
         'Tag', 'txt_manual_cat_num', ...
         'Position',[.36 py+.01-sp .1 sp], ...
         'Callback', @txt_manual_cat_num_callback);
     
 end
 
 updateManualTab(thisTab);
 end
 
 function txt_manual_cat_num_callback(hObject, eventdata, handles)
 parent = findobj('Tag', 'tab_cluster_manual');
 updateManualTab(parent);
 end
 
 function updateManualTab(parent)
 global X;
 % Add all the controls
 % Grab all the channels that we need to build the settings for
 chanIdx = getChannelIndexes();
 nChan = X.GetSize('C');
 numcat = str2num(get(findobj('Tag', 'txt_manual_cat_num'), 'String'));
 py = 0.89;
 sp = 0.05;
 
 % Make the labels for the columns but only if they do not exist already...
 if isempty(findobj('Tag', 'txt_bg'))
     uicontrol(parent,'Style','text',...
         'String','BG',...
         'Units','Normalized', ...
         'Tag', sprintf('txt_bg') , ...
         'HorizontalAlignment', 'center', ...
         'Position',[.26 py-2*sp .1 sp]);
 end
 
 for n=1:(numcat-1)
     l = findobj('Tag', sprintf('txt_thr_%d', n));
     if isempty(l)
         thrtxt(n) = uicontrol(parent,'Style','text',...
             'String',sprintf('Thr %d', n),...
             'Tag',sprintf('txt_thr_%d', n), ...
             'Units','Normalized', ...
             'HorizontalAlignment', 'center', ...
             'Position',[.26+n*.1 py-2*sp .1 sp], ...
             'Visible', 'on');
     else
         thrtxt(n) = l;
     end
    set(thrtxt(n),'Visible', 'on');
 
 end
 
 
 for k=1:nChan
     if (any(chanIdx==k))
         isEnabled = 'on';
     else
         isEnabled = 'off';
     end
     
     l = findobj('Tag', sprintf('txt_chan_%d', k));
     if isempty(l)
         txt(k) = uicontrol(parent,'Style','text',...
             'String',sprintf('Channel %d', k),...
             'Units','Normalized', ...
             'Tag', sprintf('txt_chan_%d',k) , ...
             'HorizontalAlignment', 'right', ...
             'Position',[.05 py-sp*(k+2) .2 sp]);
     else
         txt(k) = l;
     end
     set(txt(k),'Enable', isEnabled);
     
     l= findobj('Tag', sprintf('txt_manual_bg_ch_%d',k));
     if isempty(l)
         
         edt(k) = uicontrol(parent,'Style','edit',...
             'String','',...
             'Units','Normalized', ...
             'Tag', sprintf('txt_manual_bg_ch_%d',k) , ...
             'Position',[.26 py-sp*(k+2) .1 sp]);
     else
         edt(k) = l;
     end
     set(edt(k),'Enable', isEnabled);
     
     
     
     for n=1:(numcat-1)
         l = findobj('Tag', sprintf('txt_manual_cat_%d_ch_%d',n,k));
         if isempty(l)
             thr((k-1)*(numcat-1)+n) = uicontrol(parent,'Style','edit',...
                 'String','',...
                 'Units','Normalized', ...
                 'Tag', sprintf('txt_manual_cat_%d_ch_%d',n,k) , ...
                 'Position',[.26+n*.1 py-sp*(k+2) .1 sp], ...
                 'Visible', 'on');
         else
             thr((k-1)*(numcat-1)+n)= l;
         end
     set(thr((k-1)*(numcat-1)+n),'Enable', isEnabled);
     set(thr((k-1)*(numcat-1)+n),'Visible', 'on');
 
     end
     
     % Delete any columns that are no longer useful
     for n=(numcat):10
         obj = findobj('Tag', sprintf('txt_manual_cat_%d_ch_%d',n,k));
         if ~isempty(obj)
             delete(obj);
         end
         obj = findobj('Tag', sprintf('txt_thr_%d', n));
         if ~isempty(obj)
             delete(obj);
         end
     end
     
     % Add button for manual measurement
       uicontrol(parent,'Style','pushbutton','String','Fill values from spots',...
     'Units','normalized', 'Tag', 'btn_calculate_values', ...
     'Position',[.2 py-sp*(nChan+6) .4 sp*3], ...
     'Callback', @btn_calculate_values_callback);
 
     
 end
 end
 
 function makeBruteClusterTab(parent)
 tabTag = 'tab_cluster_brute_force';
 tabName = 'Brute Force';
 thisTab = findobj('Tag',tabTag);
 sp = .05;
 py = .89;
 
 if isempty(thisTab)
     thisTab = uitab('Parent', parent, 'Title', tabName, ...
         'Tag', tabTag);
     
     uicontrol(thisTab,'Style','checkbox',...
         'String','Use Brute Force Clustering',...
         'Tag', 'is_do_brute', ...
         'Units','Normalized', ...
         'HorizontalAlignment', 'right', ...
         'Position',[.05 py+sp .4 sp]);
     
     % Number of categories
     uicontrol(thisTab,'Style','text',...
         'String','Number of Categories',...
         'Units','Normalized', ...
         'HorizontalAlignment', 'right', ...
         'Position',[.05 py-sp .3 sp]);
     
     uicontrol(thisTab,'Style','edit',...
         'String','2',...
         'Units','Normalized', ...
         'Tag', 'txt_brute_cat_num', ...
         'Position',[.36 py+.01-sp .1 sp]);
+    
+    % BG Value
+    uicontrol(thisTab,'Style','text',...
+        'String','Background',...
+        'Units','Normalized', ...
+        'HorizontalAlignment', 'right', ...
+        'Position',[.05 py-2*sp .3 sp]);
+    
+    uicontrol(thisTab,'Style','edit',...
+        'String','5',...
+        'Units','Normalized', ...
+        'Tag', 'txt_brute_bg', ...
+        'Position',[.36 py+.01-2*sp .1 sp]);
+    
+    % Max Value
+    uicontrol(thisTab,'Style','text',...
+        'String','Max Threshold',...
+        'Units','Normalized', ...
+        'HorizontalAlignment', 'right', ...
+        'Position',[.05 py-3*sp .3 sp]);
+    
+    uicontrol(thisTab,'Style','edit',...
+        'String','160',...
+        'Units','Normalized', ...
+        'Tag', 'txt_brute_max', ...
+        'Position',[.36 py+.01-3*sp .1 sp]);
 end
 end
 
 function makeKMeansClusterTab(parent)
 tabTag = 'tab_cluster_kmeans';
 tabName = 'K-Means';
 thisTab = findobj('Tag',tabTag);
 sp = .05;
 py = .89;
 
 if isempty(thisTab)
     thisTab = uitab('Parent', parent, 'Title', tabName, ...
         'Tag', tabTag);
     
     uicontrol(thisTab,'Style','checkbox',...
         'String','Use K-Means clustering',...
         'Tag', 'is_do_kmeans', ...
         'Units','Normalized', ...
         'HorizontalAlignment', 'right', ...
         'Position',[.05 py+sp .4 sp]);
     
     uicontrol(thisTab,'Style','text',...
         'String','Number of clusters',...
         'Tag', 'txt_norm_kmeans', ...
         'Units','Normalized', ...
         'HorizontalAlignment', 'right', ...
         'Position',[.05 py-sp .3 sp]);
     
     uicontrol(thisTab,'Style','edit',...
         'String','15',...
         'Units','Normalized', ...
         'Tag', 'txt_kmeans_cluster_num', ...
         'Position',[.36 py+.01-sp .1 sp]);
     
     uicontrol(thisTab,'Style','checkbox',...
         'String','Separate K-Means per channel',...
         'Tag', 'is_sep_kmeans', ...
         'Units','Normalized', ...
         'HorizontalAlignment', 'right', ...
         'Position',[.05 py-3*sp .5 sp], ...
         'Callback', @is_sep_kmeans_callback);
     
     uicontrol(thisTab,'Style','text',...
         'String','Clusters per channel',...
         'Tag', 'txt_sep_kmeans', ...
         'Units','Normalized', ...
         'HorizontalAlignment', 'right', ...
         'Position',[.05 py-4*sp-.01 .3 sp]);
     
     uicontrol(thisTab,'Style','edit',...
         'String','2',...
         'Units','Normalized', ...
         'Tag', 'txt_kmeans_sep_cluster_num', ...
         'Position',[.36 py-4*sp .1 sp]);
 end
 
 end
 
 function is_sep_kmeans_callback(hObject, eventdata, handles)
 %Get object to enable or not
 sep(1) = findobj('Tag','txt_sep_kmeans');
 sep(2) = findobj('Tag','txt_kmeans_sep_cluster_num');
 
 knorm(1) = findobj('Tag','txt_norm_kmeans');
 knorm(2) = findobj('Tag','txt_kmeans_cluster_num');
 
 
 if get(hObject,'Value')
     %Disable normal KMeans Values
     knorm(1).Enable = 'off';
     knorm(2).Enable = 'off';
 
     %Enable independent KMeans Values
     sep(1).Enable = 'on';
     sep(2).Enable = 'on';
 
 else
     %Disable normal KMeans Values
     knorm(1).Enable = 'on';
     knorm(2).Enable = 'on';
 
     %Disable independent KMeans Values
     sep(1).Enable = 'off';
     sep(2).Enable = 'off';
 
 end
 
 end
 
 function makeSettingsClusterTab(parent)
 tabTag = 'tab_cluster_settings';
 tabName = 'Settings';
 thisTab = findobj('Tag',tabTag);
 sp = .05;
 py = .89;
 
 if isempty(thisTab)
     thisTab = uitab('Parent', parent, 'Title', tabName, ...
         'Tag', tabTag);
     % Allow empty clusters?
     uicontrol(thisTab,'Style','checkbox',...
         'String','No Empty Custers',...
         'Tag', 'is_no_empty_clusters', ...
         'Units','Normalized', ...
         'HorizontalAlignment', 'right', ...
         'Position',[.05 py+sp .4 sp]);
     
     % Grouping distance
     uicontrol(thisTab,'Style','text',...
         'HorizontalAlignment', 'right', ...
         'String',sprintf('%s\n%s','Groups spots','if closer than [um]'),...
         'Units','Normalized', ...
         'Position',[.05 py-sp .3 sp+0.02]);
     
     uicontrol(thisTab,'Style','edit',...
         'String','8.5',...
         'Units','Normalized', ...
         'Tag', 'txt_grouping_distance', ...
         'Position',[.36 py+.01-sp .1 sp]);
     
     % Z Compensation
     uicontrol(thisTab,'Style','text',...
         'String','Z Compensation factor',...
         'Units','Normalized', ...
         'HorizontalAlignment', 'right', ...
         'Position',[.05 py-2*sp .3 sp]);
     
     uicontrol(thisTab,'Style','edit',...
         'String','3',...
         'Units','Normalized', ...
         'Tag', 'txt_z_compensation_factor', ...
         'Position',[.36 py+.01-2*sp .1 sp]);
 end
 
 end
 
 
 function makeReassignTab(parent)
 tabTag = 'tab_reassign';
 tabName = 'Reassign';
 thisTab = findobj('Tag',tabTag);
 sp = .05;
 h= 0.05;
 py = .89;
 
 if isempty(thisTab)
     thisTab = uitab('Parent', parent, 'Title', tabName, ...
         'Tag', tabTag);
     % Make one spot per cluster, spot number is cluster size?
     uicontrol(thisTab,'Style','checkbox',...
         'String','Make 1 Spot / Subcluster',...
         'Tag', 'is_reassign_single_spot', ...
         'Units','Normalized', ...
         'HorizontalAlignment', 'right', ...
         'Position',[.05 py+sp .4 h]);
     
     % Grouping distance
     uicontrol(thisTab,'Style','text',...
         'HorizontalAlignment', 'right', ...
         'String','Maximum distance for reassignment [um]',...
         'Units','Normalized', ...
         'Position',[.05 py-sp .5 h]);
     
     uicontrol(thisTab,'Style','edit',...
         'String','8.5',...
         'Units','Normalized', ...
         'Tag', 'txt_reassign_max_distance', ...
         'Position',[.56 py-sp .1 h]);
     
     % Z Compensation
     uicontrol(thisTab,'Style','text',...
         'String','Maximum intensity distance [AU]',...
         'Units','Normalized', ...
         'HorizontalAlignment', 'right', ...
         'Position',[.05 py-2*sp .5 h]);
     
     uicontrol(thisTab,'Style','edit',...
         'String','120',...
         'Units','Normalized', ...
         'Tag', 'txt_reassign_max_intensity', ...
         'Position',[.56 py-2*sp .1 h]);
     
     % Z Compensation
     uicontrol(thisTab,'Style','text',...
         'String','Reassign if smaller than',...
         'Units','Normalized', ...
         'HorizontalAlignment', 'right', ...
         'Position',[.05 py-3*sp .5 h]);
     
     uicontrol(thisTab,'Style','edit',...
         'String','10',...
         'Units','Normalized', ...
         'Tag', 'txt_reassign_cluster_min', ...
         'Position',[.56 py-3*sp .1 h]);
 end
 end
 
 function makeWingJTab(parent)
 tabTag = 'tab_wing_j';
 tabName = 'WingJ';
 thisTab = findobj('Tag',tabTag);
 sp = .05;
 py = .89;
 h  = .05;
 if isempty(thisTab)
     thisTab = uitab('Parent', parent, 'Title', tabName, ...
         'Tag', tabTag);
     
     % Make one spot per cluster, spot number is cluster size?
     uicontrol(thisTab,'Style','checkbox',...
         'String','Remove Offset',...
         'Tag', 'is_wingj_remove_offset', ...
         'Units','Normalized', ...
         'HorizontalAlignment', 'right', ...
         'Position',[.05 py .4 h]);
     
         uicontrol(thisTab,'Style','checkbox',...
         'String','Flip Y Coordinate',...
         'Tag', 'is_wingj_flip_y', ...
         'Units','Normalized', ...
         'HorizontalAlignment', 'right', ...
         'Position',[.05 py-sp .4 h]);
     
 end
 end
 
 %% Callbacks for all buttons
 function btn_refresh_callback(hObject, eventdata, handles)
 
 end
 
 function btn_sum_callback(hObject, eventdata, handles)
 sumChannels();
 end
 
 function btn_clear_outside_callback(hObject, eventdata, handles)
 clearOutside();
 end
 
 function btn_detect_spots_callback(hObject, eventdata, handles)
 detectSpots();
 end
 
 function btn_cluster_spots_callback(hObject, eventdata, handles)
 clusterSpots();
 end
 
 function btn_reassign_spots_callback(hObject, eventdata, handles)
 reassignSpots();
 end
 
 function btn_export_callback(hObject, eventdata, handles)
 exportToCSV();
 end
 
 function savebtn_callback(hObject, eventdata, handles)
 saveSettings();
 end
 
 function loadbtn_callback(hObject, eventdata, handles)
 % Make sure this function is generic enough
 loadSettings();
 end
 
 function btn_calculate_values_callback(hObject, eventdata, handles)
 manualAverageInterface();
 end
 
 function btn_wingj_callback(hObject, eventdata, handles)
 loadWingJData();
 end
 
 
 
diff --git a/functions/clusterDistances.m b/functions/clusterDistances.m
index 5616767..50b35da 100644
--- a/functions/clusterDistances.m
+++ b/functions/clusterDistances.m
@@ -1,45 +1,44 @@
 function clusterDistances( spotData, clusterIndexes, zComp, minDist, parent )
 
 global X;
-
 color = createLUT(max(clusterIndexes), 255);
 for clus = 1:max(clusterIndexes)
     
     % Get indices of spots belonging to cluster clus
     clusInd = find(clusterIndexes == clus);
     nSpots(clus) = numel(clusInd);
     
     
     spotPositions = spotData.posXYZ(clusInd,:);
     % Cluster could be empty
     if ~isempty(spotPositions)
         
         clusterSpotsFolder = X.CreateGroup(sprintf('Cluster %d', clus));
         X.AddToScene(clusterSpotsFolder, 'Parent', parent);
         % compensate Z
         spotPositions(:,3) = spotPositions(:,3) / zComp;
         
         % Easy to get subclusters by distance
         if size(spotPositions, 1) > 1
             T = clusterdata(spotPositions,'criterion', 'distance', 'distance', 'euclidean', 'cutoff', minDist);
         else
             T = 1;
         end
         
         % Get the IDs for each cluster and make a spot
         subclusIds = unique(T);
         for subClus = subclusIds'
             idx = find(T==subClus);
             tempSpot = X.CreateSpots(spotData.posXYZ(clusInd(idx),:), spotData.radii(clusInd(idx),1)', 'Name', sprintf('Subcluster %d', subClus));
             X.SetColor(tempSpot, color(clus,:));
             X.AddToScene(tempSpot, 'Parent',clusterSpotsFolder);
         end
         ns=length(subclusIds);
         
         disp(sprintf(' Cluster %d: %d Subclusters: %d Spots', clus, ns, nSpots(clus)));
     end
 end
 
 
 end
 
diff --git a/functions/clusterSpots.m b/functions/clusterSpots.m
index 2e2e89c..9156750 100644
--- a/functions/clusterSpots.m
+++ b/functions/clusterSpots.m
@@ -1,160 +1,163 @@
 function clusterSpots()
 
 global X;
 
 % Get the kind of clustering we will be doing
 is_do_manual = getFromTag('is_do_manual');
 is_do_brute  = getFromTag('is_do_brute');
 is_do_kmeans = getFromTag('is_do_kmeans');
 
 % Grab the Spot Object in the Scene
 nS = X.GetNumberOf('Spots');
 if nS > 1
     [~, nS] = X.SelectDialog('Spots');
 end
 spots = X.GetObject('Type', 'Spots', 'Number', nS);
 
 % Grab the channels we will be using
 chanIdx = getChannelIndexes();
 
 % Grab the stats we need, namely Intensity Mean
 spotsData = X.GetSelectedStatistics(spots, 'Intensity Mean');
 
 % To cluster, we need an nx2 array with
 % col1: spotID
 % col2: Value of selected statistic
 % Get the indices of the chosen statistic
 
 % Build what we need
 selectedIds      = spotsData.ids+1;
 selectedChannels = cell2mat(spotsData.factors(:,2));
 selectedValues   = spotsData.values;
 
 
 % for all the Ids and all Channels, will fill all values from the chosen statistic
 for  i = 1:length(selectedValues)
     fullSpotsDataForCluster(selectedIds(i),str2num(selectedChannels(i))) = selectedValues(i);
 end
 
 % Finished data for clustering
 spotsClusterData = fullSpotsDataForCluster(:,chanIdx);
 
 % Clear some memory
 fullSpotsDataForCluster = [];
 
 %Spot Grouping
 spotGrouping = getFromTag('txt_grouping_distance', 'Number');
 
 % Z compensation
 zComp = getFromTag('txt_z_compensation_factor', 'Number');
 
 % Grouping Distance for after clustering
 minDist = getFromTag('txt_grouping_distance', 'Number');
 
 if is_do_manual
     % Just grab all the channels and all the values and then use the
     % equivalent of the brute-force to get the results
     % How many categories per channel
     nCat = getFromTag('txt_manual_cat_num', 'Number');
     % Make an array of edges for each channel
     edges = zeros(numel(chanIdx), nCat+2); % +2 to include 0 and Infinity
     edges(:,end) = Inf;
     
     % Everything in double loop, first channels
     for c=1:numel(chanIdx)
         %get BG
         edges(c,2) = getFromTag(sprintf('txt_manual_bg_ch_%d',chanIdx(c)), 'Number');
         % Now for each category
         for n=1:(nCat-1)
             edges(c,2+n) = getFromTag(sprintf('txt_manual_cat_%d_ch_%d',n,chanIdx(c)), 'Number');
         end
     end
     
     [edges, clusterIndexes ] = sortManual(spotsClusterData, edges);
 
     % create a Parent folder with the Cluster Number
     manualFolder = X.CreateGroup(sprintf('Manual Clustering %d categories per channel, Z Compensation [%d]', nCat, zComp ));
     X.AddToScene(manualFolder);
     
     
     clusterDistances(spotsData, clusterIndexes, zComp, minDist, manualFolder);
     disp('Manual Clustering DONE');
     edges
     
 end
 
 if is_do_brute
     % Here we use a very simple method to cluster them :
     % Check on each channel for the intensities and categorise them. a
     % binning into N categories for each channel.
     nCat = getFromTag('txt_brute_cat_num', 'Number');
-    [centroids, clusterIndexes ] = sortBrute(spotsClusterData, nCat, 160, 10);
+    max = getFromTag('txt_brute_max', 'Number');
+    bg = getFromTag('txt_brute_bg', 'Number');
+
+[centroids, clusterIndexes ] = sortBrute(spotsClusterData, nCat, max, bg);
     
     % create a Parent folder with the Cluster Number
-    bruteFolder = XT.CreateGroup(sprintf('Brute Force Clustering %d categories per channel, Z Compensation [%d]', nCat, zComp ));
-    XT.AddToScene(bruteFolder);
+    bruteFolder = X.CreateGroup(sprintf('Brute Force Clustering %d categories per channel, Z Compensation [%d]', nCat, zComp ));
+    X.AddToScene(bruteFolder);
     
     clusterDistances(spotsData, clusterIndexes, zComp, minDist, bruteFolder);
     disp('Brute Force Clustering DONE');
     centroids
 end
 
 if is_do_kmeans
     % Use separate clusterings per channel?
     is_sep_kmeans = getFromTag('is_sep_kmeans');
     
     if is_sep_kmeans
         nClusterPerChannel = getFromTag('txt_kmeans_sep_cluster_num', 'Number');
         opts = statset('Display','final');
         str = '';
         for i=1:numel(chanIdx)
             [clusterIndexes(:,i), centroids(:,i)] = kmeans(spotsClusterData(:,i),nClusterPerChannel,...
                 'start','plus',...
                 'replicates',50,...
                 'emptyaction','drop',...
                 'Options',opts);
             
             str = [str '%d'];
         end
              
         [C ia ic] = unique(clusterIndexes, 'rows');
         
         % for the indexes, make a new array from 1 to to numger of unique
         % rows
         newIdx = 1:size(C,1);
         
         % Get the centroids
         cent = [];
         for c=1:numel(chanIdx)
             cent = [cent centroids(C(:,c),c)];
         end
         centroids = cent
         % create a Parent folder with the Cluster Number
         sepkMeansFolder = X.CreateGroup(sprintf('Separate K-Means With %d Clusters per Channel, Z Compensation [%d]', nClusterPerChannel, zComp ));
         X.AddToScene(sepkMeansFolder);
         clusterDistances(spotsData, newIdx(ic), zComp, minDist, sepkMeansFolder);
         
     else
         
         nClusters = getFromTag('txt_kmeans_cluster_num', 'Number');
         
         opts = statset('Display','final');
         
         [clusterIndexes, centroids] = kmeans(spotsClusterData,nClusters,...
             'start','plus',...
             'replicates',50,...
             'emptyaction','drop',...
             'Options',opts);
         
         % create a Parent folder with the Cluster Number
         kMeansFolder = X.CreateGroup(sprintf('K-Means With %d Clusters, Z Compensation [%d]', nClusters, zComp ));
         X.AddToScene(kMeansFolder);
         
         clusterDistances(spotsData, clusterIndexes, zComp, minDist, kMeansFolder);
         disp('K-Means Clustering DONE');
         
     end
     centroids
 end
 end
 
diff --git a/functions/manualAverageInterface.m b/functions/manualAverageInterface.m
index b3ec6c6..120e1c5 100644
--- a/functions/manualAverageInterface.m
+++ b/functions/manualAverageInterface.m
@@ -1,114 +1,129 @@
 function manualAverageInterface
 global X;
 global intensities;
+global res;
+
+% Get all the spots first
+sCh = getFromTag('txt_channel_spot', 'Number');
+spots = X.GetObject('Name', sprintf('Detected Spots from Channel %d', sCh));
+stats = X.GetSelectedStatistics(spots, 'Intensity Mean');
+
+selectedChannels = cell2mat(stats.factors(:,2))
+intensities = [];
+% for all the Ids and all Channels, will fill all values from the chosen statistic
+for  i = 1:length(stats.values)
+    intensities(stats.ids(i)+1, str2num(selectedChannels(i))) = stats.values(i);
+end
+
 f = figure('Name', 'BIOP - Spots Stats', ...
     'NumberTitle', 'off', 'Visible', 'off', 'Position', [0 0 500 200], ...
     'Tag', 'main_f', ...
     'DockControls', 'off', 'ToolBar', 'none', 'MenuBar', 'none');
 
 % Move the window to the center of the screen.
 movegui(f,'center');
 
 % Make the window visible.
 f.Visible = 'on';
 
 l = .05;
 w = .4;
 h = .1;
 s = 0.1;
 % Refresh button
 uicontrol(f,'Style','pushbutton','String','Calculate',...
     'Units','normalized', 'Tag', 'btn_stats_refresh', ...
     'Position',[0.10 .75 0.8 h*2],...
     'Callback', @btn_stats_refresh_callback);
 % Info text
 uicontrol(f,'Style','text','String','Spots Selected: ',...
     'Units','normalized', ...
     'HorizontalAlignment', 'right', ...
     'Position',[l .60 0.32 h]);
 uicontrol(f,'Style','text','String','',...
     'Units','normalized', 'Tag', 'txt_spot_name', ...
     'HorizontalAlignment', 'left', ...
     'Position',[l+0.33 .60 0.5 h]);
 
 uicontrol(f,'Style','text','String','',...
     'Units','normalized', 'Tag', 'txt_spot_stats', ...
     'FontWeight', 'bold', ...
     'HorizontalAlignment', 'left', ...
     'Position',[0.26 .44 0.9 h]);
 
 % 'Add to' popup list
 options = {};
 chan={};
 nChan  = getChannelIndexes();
 manCat = getFromTag('txt_manual_cat_num', 'Number');
 for i=nChan
     chan{end+1} = sprintf('Channel %d', i);
     options{end+1} = sprintf('Channel %d BG',i);
     for j=1:(manCat-1)
         options{end+1} = sprintf('Channel %d Thr %d',i,j);
     end
 end
 
 
 %Choose Channel
 uicontrol(f, 'Style', 'popup',...
     'Units','normalized', 'Tag', 'popup_chan', ...
     'String', chan,...
     'Position',[l .45 0.2 h]);
        
 
 uicontrol(f, 'Style', 'popup',...
     'Units','normalized', 'Tag', 'popup_add_to', ...
     'String', options,...
     'Position',[l .15 0.5 h]);
        
 % Add to button
 uicontrol(f,'Style','pushbutton','String','Add',...
     'Units','normalized', 'Tag', 'btn_add', ...
     'Position',[l+0.55 .15 0.2 .1],...
     'Callback', @btn_add_callback);
 end
 
 
 
 function btn_stats_refresh_callback(hObject, eventdata, handles)
 global X;
 global intensities;
+global res;
+
 choices = get(findobj('Tag', 'popup_chan'),'String');
-choice = choices{getFromTag('popup_chan')}
+choice = choices{getFromTag('popup_chan')};
 
 expression = 'Channel (?<channel>\d+)';
 tokenNames = regexp(choice,expression,'names');
-
+ch = str2num(tokenNames.channel(1));
 
 spots = X.GetObject();
-
-idx = spots.GetSelectedIndices();
-stats = X.GetSelectedStatistics(spots, 'Intensity Mean', 'Channel', str2num(tokenNames.channel(1)))
-intensities = stats.values(idx+1);
+idx = spots.GetSelectedIndices()+1;
+size(intensities);
+res = intensities(idx,ch);
 setFromTag('txt_spot_name', X.GetName(spots));  
-setFromTag('txt_spot_stats', sprintf('%d Spots, Average Intensity %.1f', numel(intensities), mean(intensities)));
+setFromTag('txt_spot_stats', sprintf('%d Spots, Average Intensity %.2f', numel(res), mean(res)));
 
 
 end
 
 function btn_add_callback(hObject, eventdata, handles)
 % Get popup options
 global intensities;
-
+global res;
 choices = get(findobj('Tag', 'popup_add_to'),'String');
 choice = choices{getFromTag('popup_add_to')};
 
 expression = ['Channel (?<channel>\d+) [BGThr ]+(?<cat>[\d]*).*'];
 tokenNames = regexp(choice,expression,'names');
 
 if isempty(tokenNames.cat)
     %BG
-    setFromTag(sprintf('txt_manual_bg_ch_%s',tokenNames.channel(1)), sprintf('%.1f',mean(intensities)));
+    setFromTag(sprintf('txt_manual_bg_ch_%s',tokenNames.channel(1)), sprintf('%.2f',mean(res)));
 else
-    setFromTag(sprintf('txt_manual_cat_%s_ch_%s',tokenNames.cat(1), tokenNames.channel(1)), sprintf('%.1f',mean(intensities)));
+    setFromTag(sprintf('txt_manual_cat_%s_ch_%s',tokenNames.cat(1), tokenNames.channel(1)), sprintf('%.2f',mean(res)));
 end
 
 
 end
\ No newline at end of file
diff --git a/functions/sortBrute.m b/functions/sortBrute.m
index bfb7d13..bbacbac 100644
--- a/functions/sortBrute.m
+++ b/functions/sortBrute.m
@@ -1,24 +1,27 @@
 function [ centroids, finalIdx ] = sortBrute(data, nCat, theMax, bg) 
     
 % Divide the Max by the number of categories
 step = (theMax-bg) / (nCat);
 
 edges = bg:step:(step*nCat);
 edges = [0 edges Inf];
 
 finalIdx = zeros(size(data,1),1);
 
 for i=1:size(data,2)
     [~, idx] = histc(data(:,i), edges);
     idx(idx==0) = 1;
     finalIdx(:,i) = idx;
     
 end
+[C ia ic] = unique(finalIdx, 'rows');
+uClusters = C;
+% for the indexes, make a new array from 1 to to numger of unique
+% rows
+newIdx = 1:size(C,1);
+centroids = [];
 
-[uClusters] = unique(finalIdx, 'rows');
+finalIdx = newIdx(ic)';
 
-% Index each row of data.
-
-%Return the centroids
 centroids = (uClusters-1)*step - step/2 + bg;
 centroids(uClusters==1) = bg/2;
\ No newline at end of file