diff --git a/sc/experiment/classes/@ScFile/get_triggables.m b/sc/experiment/classes/@ScFile/get_triggables.m
new file mode 100644
index 0000000..6705961
--- /dev/null
+++ b/sc/experiment/classes/@ScFile/get_triggables.m
@@ -0,0 +1,18 @@
+function triggable = get_triggables(obj)
+
+triggable = {};
+
+for i=1:obj.signals.n
+  
+  signal = obj.signals.get(i);
+  
+  if signal.waveforms.n > 0
+    triggable = add_to_list(triggable, signal);
+  end
+  
+end
+
+triggable = concat_list(triggable, obj.stims.cell_list);
+triggable = concat_list(triggable, obj.textchannels.cell_list);
+
+end
\ No newline at end of file
diff --git a/sc/experiment/classes/@ScSignal/ScSignal.m b/sc/experiment/classes/@ScSignal/ScSignal.m
index f41618d..0a39a68 100644
--- a/sc/experiment/classes/@ScSignal/ScSignal.m
+++ b/sc/experiment/classes/@ScSignal/ScSignal.m
@@ -1,4 +1,5 @@
-classdef ScSignal < ScChannel & ScDynamicClass & sc_experiment.EmptyClassPlaceholder
+classdef ScSignal < ScChannel & ScDynamicClass & sc_experiment.EmptyClassPlaceholder & ...
+  sc_experiment.Triggable
   
   methods (Static)
     empty_class = make_empty_class()
diff --git a/sc/experiment/classes/@ScSignal/get_tags.m b/sc/experiment/classes/@ScSignal/get_tags.m
new file mode 100644
index 0000000..6793eba
--- /dev/null
+++ b/sc/experiment/classes/@ScSignal/get_tags.m
@@ -0,0 +1,5 @@
+function val = get_tags(obj)
+
+val = obj.waveforms.values('tag');
+
+end
\ No newline at end of file
diff --git a/sc/experiment/classes/ScStim.m b/sc/experiment/classes/ScStim.m
index 2eafb0a..2d816be 100644
--- a/sc/experiment/classes/ScStim.m
+++ b/sc/experiment/classes/ScStim.m
@@ -1,51 +1,88 @@
-classdef ScStim < ScChannel
-
+classdef ScStim < ScChannel & sc_experiment.Triggable
+  
   properties
+    
     triggers
     istrigger
+    
   end
-
+  
   methods
+    
     function obj = ScStim(parent, channelname,varargin)
+      
       obj.parent  = parent;
       obj.channelname = channelname;
       obj.istrigger = false;
+      
       for k=1:2:numel(varargin)
         obj.(varargin{k}) = varargin{k+1};
       end
+      
     end
-
+    
+    
     function sc_loadtimes(obj)
+      
       obj.triggers = ScList();
+      
       if isempty(who('-file',obj.parent.filepath,obj.channelname))
+        
         fprintf('Warning: Could not find channel %s in file %s\n',obj.channelname,obj.parent.filepath);
         return
+        
       end
-      d = load(obj.parent.filepath,obj.channelname);
+      
+      d = load(obj.parent.filepath, obj.channelname);
       times = d.(obj.channelname).times;
+      
       if isfield(d.(obj.channelname),'codes')
+        
         codes = d.(obj.channelname).codes;
         uniquecodes = unique(codes,'rows');
+        
         for i=1:size(uniquecodes,1)
+          
           rows = all(codes == repmat(uniquecodes(i,:),size(codes,1),1),2);
           tag = num2str(uniquecodes(i,:));
           pos = isspace(tag);
           tag = tag(~pos);
-          obj.triggers.add(ScSpikeTrain(tag,times(rows)));
+          obj.triggers.add(ScSpikeTrain(tag, times(rows)));
+          
         end
+        
       else
-        obj.triggers.add(ScSpikeTrain(obj.tag,times))
+        
+        obj.triggers.add(ScSpikeTrain(obj.tag, times))
+        
       end
+      
     end
-
+    
+    
     function sc_clear(obj)
+      
       obj.triggers = ScList;
+      
     end
-
+    
+    
+    function val = get_tags(obj)
+      
+      val = obj.triggers.values('tag');
+      
+    end
+    
   end
+  
   methods (Static)
+    
     function obj = loadobj(a)
+      
       obj = loadobj@ScChannel(a);
+      
     end
+    
   end
+  
 end
diff --git a/sc/experiment/classes/ScTextMark.m b/sc/experiment/classes/ScTextMark.m
index 69617ba..d47839f 100644
--- a/sc/experiment/classes/ScTextMark.m
+++ b/sc/experiment/classes/ScTextMark.m
@@ -1,37 +1,54 @@
 classdef ScTextMark < ScChannel & ScTriggerParent
   
   methods
+    
     function obj = ScTextMark(parent, channelname,varargin)
-      obj.parent = parent;
+      
+      obj.parent      = parent;
       obj.channelname = channelname;
-      obj.triggers = ScList;
+      obj.triggers    = ScList;
+      
       for k=1:2:numel(varargin)
         obj.(varargin{k}) = varargin{k+1};
       end
+      
     end
     
+    
     %Load digital channel values
     function sc_loadtimes(obj)
+      
       obj.triggers = ScList;
+      
       if isempty(who('-file',obj.parent.filepath,obj.channelname))
+        
         fprintf('Warning: Could not find channel %s in file %s\n',obj.channelname,obj.parent.filepath);
         return
+        
       end
+      
       d = load(obj.parent.filepath,obj.channelname);
+      
       if isfield(d.(obj.channelname),'text')
+        
         times = d.(obj.channelname).times;
         text = d.(obj.channelname).text;
         cellstr = cell(size(times));
+        
         for i=1:numel(cellstr)
           cellstr(i) = {deblank(text(i,:))};
         end
+        
         tags = unique(cellstr);
         obj.triggers = ScList;
+        
         for i=1:numel(tags)
+          
           pos = cellfun(@(x) strcmp(x,tags{i}), cellstr);
           tagtimes = times(pos);
           
           if obj.parent.stims.has('tag','DigMark')
+            
             trigger = obj.parent.stims.get('tag','DigMark').triggers.get('tag','1000');
             
             if isempty(trigger)
@@ -39,17 +56,35 @@ function sc_loadtimes(obj)
             end
             
             digmarktimes = obj.parent.stims.get('tag','DigMark').triggers.get('tag','1000').gettimes(-inf,inf);
+            
             for j=1:numel(tagtimes)
+              
               [~,ind] = min(abs(tagtimes(j)-digmarktimes));
               tagtimes(j) = digmarktimes(ind);
+              
             end
+            
           end
+          
           obj.triggers.add(ScSpikeTrain(tags{i},tagtimes));
+          
         end
+        
       end
+      
+    end
+    
+    
+    function val = get_tags(obj)
+      
+      val = obj.triggers.values('tag');
+      
     end
+    
   end
+  
   methods (Static)
+    
     function obj = loadobj(a)
       obj = loadobj@ScChannel(a);
     end
diff --git a/sc/viewer/classes/panels/@AmplitudeComputedChannel/AmplitudeComputedChannel.m b/sc/viewer/classes/panels/@AmplitudeComputedChannel/AmplitudeComputedChannel.m
index de00924..b8d996a 100644
--- a/sc/viewer/classes/panels/@AmplitudeComputedChannel/AmplitudeComputedChannel.m
+++ b/sc/viewer/classes/panels/@AmplitudeComputedChannel/AmplitudeComputedChannel.m
@@ -21,7 +21,7 @@ function plot_amplitude(obj)
 
       start = intra_get_amplitude_pseudo_start(amplitude);
       stop = intra_get_amplitude_pseudo_stop(amplitude, obj.gui.main_channel.v);
-      is_pseudo = intra_is_amplitude_data_pseudo(amplitude);
+      is_pseudo = ~amplitude.valid_data;
       rise = intra_get_amplitude_pseudo_rise(start, stop, is_pseudo, ...
         amplitude, obj.gui.main_channel.v);
       middle = intra_get_middle_index(rise, .1);
diff --git a/sc2/+sc_experiment/Triggable.m b/sc2/+sc_experiment/Triggable.m
new file mode 100644
index 0000000..813b1a7
--- /dev/null
+++ b/sc2/+sc_experiment/Triggable.m
@@ -0,0 +1,7 @@
+classdef Triggable < handle
+  
+  methods (Abstract)
+    varargout = get_tags(varargin)
+  end
+  
+end
\ No newline at end of file
diff --git a/sc2/sc-viewer/panels/+sc_viewer/@ScExperimentPanel/ScExperimentPanel.m b/sc2/sc-viewer/panels/+sc_viewer/@ScExperimentPanel/ScExperimentPanel.m
index e1fac54..a95d990 100644
--- a/sc2/sc-viewer/panels/+sc_viewer/@ScExperimentPanel/ScExperimentPanel.m
+++ b/sc2/sc-viewer/panels/+sc_viewer/@ScExperimentPanel/ScExperimentPanel.m
@@ -127,7 +127,13 @@ function signal1_callback(obj)
     function signal2_callback(obj)
       
       indx = get(obj.ui_signal2, 'Value');
-      obj.viewer.set_signal2(obj.viewer.file.signals.get(indx));
+      signals = obj.viewer.file.signals;
+      
+      if indx <= length(signals)
+        obj.viewer.set_signal2(signals(indx));
+      else
+        obj.viewer.set_signal2([]);
+      end
       
     end
     
@@ -175,7 +181,9 @@ function file_listener(obj)
         end
         
       else
+        
         set(obj.ui_file, 'Visible', 'off');
+      
       end
       
     end
@@ -226,20 +234,17 @@ function signal1_listener(obj)
     
     function signal2_listener(obj)
       
-      if ~isempty(obj.viewer.signal2)
+      str  = obj.viewer.file.signals.values('tag');
+      str  = add_to_list(str, '#none');
         
-        str  = obj.viewer.file.signals.values('tag');
-        indx = find(@(x) strcmp(x, obj.viewer.signal2.tag), str);
+      if ~isempty(obj.viewer.signal2)
         
-        if ~isempty(indx)
-          set(obj.ui_signal2, 'String', str, 'Value', indx, 'Visible', 'on');
-        else
-          set(obj.ui_signal2, 'Visible', 'off');
-        end
+        indx = find(@(x) strcmp(x, obj.viewer.signal2.tag), str);        
+        set(obj.ui_signal2, 'String', str, 'Value', indx, 'Visible', 'on');
         
       else
         
-        set(obj.ui_signal2, 'Visible', 'off');
+        set(obj.ui_signal2, 'String', str, 'Value', length(str), 'Visible', 'on');
         
       end
       
diff --git a/sc2/sc-viewer/panels/+sc_viewer/@ScTriggerPanel/ScTriggerPanel.m b/sc2/sc-viewer/panels/+sc_viewer/@ScTriggerPanel/ScTriggerPanel.m
index c68440b..f0576da 100644
--- a/sc2/sc-viewer/panels/+sc_viewer/@ScTriggerPanel/ScTriggerPanel.m
+++ b/sc2/sc-viewer/panels/+sc_viewer/@ScTriggerPanel/ScTriggerPanel.m
@@ -17,7 +17,7 @@
     
     function ui_panel = get_panel(viewer)
       
-      ui_panel = uipanel(viewer.button_window, 'Title', 'Experiment');
+      ui_panel = uipanel(viewer.button_window, 'Title', 'Trigger');
       panel    = sc_viewer.ScTriggerPanel(ui_panel, viewer);
       mgr      = sc_layout.PanelLayoutManager(ui_panel);
       
@@ -39,11 +39,6 @@
       panel.ui_tot_trigger_nbr = mgr.add(sc_ctrl('text', ''), 200);
       mgr.newline();
       
-      mgr.add(sc_ctrl('text', 'Trigger #'), 100);
-      panel.ui_trigger_indx = mgr.add(sc_ctrl('edit', [], ...
-        @(~,~) panel.trigger_indx_callback(), 'Visible', 'off'), 100);
-      mgr.newline();
-      
       mgr.add(sc_ctrl('text', 'trigger_increment'), 100);
       panel.ui_trigger_increment = mgr.add(sc_ctrl('edit', [], ...
         @(~,~) panel.trigger_increment_callback(), 'Visible', 'off'), 100);
@@ -74,30 +69,18 @@
       
       mgr.trim();
       
-      sc_addlistener(viewer, 'trigger_parent', ...
-        @(~,~) panel.trigger_parent_listener(), ui_panel);
-      
-      sc_addlistener(viewer, 'trigger_tag', ...
-        @(~,~) panel.trigger_tag_listener(), ui_panel);
-      
-      sc_addlistener(viewer, 'trigger_time', ...
-        @(~,~) panel.trigger_time_listener(), ui_panel);
-      
-      sc_addlistener(viewer, 'pretrigger', ...
-        @(~,~) panel.pretrigger_listener(), ui_panel);
-      
-      sc_addlistener(viewer, 'posttrigger', ...
-        @(~,~) panel.posttrigger_listener(), ui_panel);
-      
-      sc_addlistener(viewer, 'trigger_increment', ...
-        @(~,~) panel.incremnent_listener(), ui_panel);
-      
       panel.trigger_parent_listener();
       panel.trigger_tag_listener();
       panel.trigger_time_listener();
       panel.pretrigger_listener();
       panel.posttrigger_listener();
       
+      sc_addlistener(panel.viewer, 'trigger_parent', @(~,~) panel.trigger_parent_listener, ui_panel);
+      sc_addlistener(panel.viewer, 'trigger_tag', @(~,~) panel.trigger_tag_listener, ui_panel);
+      sc_addlistener(panel.viewer, 'trigger_time', @(~,~) panel.trigger_time_listener, ui_panel);
+      sc_addlistener(panel.viewer, 'pretrigger', @(~,~) panel.pretrigger_listener, ui_panel);
+      sc_addlistener(panel.viewer, 'posttrigger', @(~,~) panel.posttrigger_listener, ui_panel);
+    
     end
     
   end
@@ -113,27 +96,82 @@
   methods (Access = protected)
     
     function trigger_parent_listener(obj)
-      error('Not implemented');
+      
+      triggables = obj.viewer.file.get_triggables();
+      str = get_values(triggables, 'tag');
+      str = add_to_list(str, '#none');
+      
+      if isempty(obj.viewer.trigger_parent)
+        indx = length(str);
+      else
+        indx = find(cellfun(@(x) x == obj.viewer.trigger_parent, triggables));
+      end
+      
+      set(obj.ui_trigger_parent, 'String',str, 'Value', indx, ...
+        'Visible', 'on');
+      
     end
     
     
     function trigger_tag_listener(obj)
-      error('Not implemented');
+      
+      if isempty(obj.viewer.trigger_tag)
+        
+        set(obj.ui_trigger_tag, 'Visible', 'off');
+        return
+        
+      end
+      
+      str = obj.viewer.trigger_parent.get_tags();
+      indx = find(cellfun(@(x) strcmp(x, obj.viewer.trigger_tag), str));
+      
+      set(obj.ui_trigger_tag, 'String', str, ...
+        'Value', indx, 'Visible', 'on');
+      
     end
     
     
     function trigger_time_listener(obj)
-      error('Not implemented');
+      
+      set(obj.ui_trigger_time, 'String', obj.viewer.trigger_time);
+      
     end
     
     
     function pretrigger_listener(obj)
-      error('Not implemented');
+      
+      set(obj.ui_trigger_time, 'String', obj.viewer.pretrigger);
+      
     end
     
     
     function posttrigger_listener(obj)
-      error('Not implemented');
+      
+      set(obj.ui_trigger_time, 'String', obj.viewer.pretrigger);    
+    
+    end
+    
+    
+    function trigger_parent_callback(obj)
+      
+      indx = get(obj.ui_trigger_parent, 'Value');
+      triggables = obj.viewer.file.get_triggables();
+      
+      if indx > length(triggables)
+        obj.viewer.set_trigger_parent([]);
+      else
+        obj.viewer.set_trigger_parent(triggables{indx});
+      end
+      
+    end
+    
+    
+    function trigger_tag_callback(obj)
+      
+      indx = get(obj.ui_trigger_parent, 'Value');
+      tags = obj.viewer.trigger_parent.get_tags();
+      obj.viewer.set_trigger_tag(tags{indx});
+      
     end
     
   end
diff --git a/sc2/sc-viewer/viewer/+sc_viewer/@ScButtonViewer/show.m b/sc2/sc-viewer/viewer/+sc_viewer/@ScButtonViewer/show.m
index df8990d..0a456bb 100644
--- a/sc2/sc-viewer/viewer/+sc_viewer/@ScButtonViewer/show.m
+++ b/sc2/sc-viewer/viewer/+sc_viewer/@ScButtonViewer/show.m
@@ -6,22 +6,22 @@ function show(obj)
 end
 
 set(obj.button_window, 'ToolBar', 'None', 'MenuBar', 'none');
-set(obj.button_window, 'CloseRequestFcn', @(~,~) obj.close_request);
+set(obj.plot_window, 'CloseRequestFcn', @(~,~) obj.close_request);
 set(obj.button_window,  'Tag',            sc_viewer.ScViewer.figure_tag)
 
 if isempty(obj.plot_window) || ~ishandle(obj.plot_window)
   obj.plot_window = figure;
 end
 
-clf(obj.plot_window,   'reset');
-set(obj.plot_window,   'Tag', sc_viewer.ScViewer.figure_tag)
+clf(obj.plot_window, 'reset');
+set(obj.plot_window, 'Tag', sc_viewer.ScViewer.figure_tag)
 
 mgr = sc_layout.FigureLayoutManager(obj.button_window);
 mgr.add(sc_viewer.ScUserInfoPanel.get_panel(obj), 200);
 mgr.newline();
 mgr.add(sc_viewer.ScExperimentPanel.get_panel(obj), 200);
-%mgr.newline();
-%mgr.add(sc_viewer.ScTriggerPanel.get_panel(obj));
+mgr.newline();
+mgr.add(sc_viewer.ScTriggerPanel.get_panel(obj), 200);
 
 mgr.trim();
 
diff --git a/sc2/sc-viewer/viewer/+sc_viewer/@ScPlotViewer/close_request.m b/sc2/sc-viewer/viewer/+sc_viewer/@ScPlotViewer/close_request.m
new file mode 100644
index 0000000..76640cf
--- /dev/null
+++ b/sc2/sc-viewer/viewer/+sc_viewer/@ScPlotViewer/close_request.m
@@ -0,0 +1,14 @@
+function close_request(obj)
+
+
+if obj.has_unsaved_changes
+  
+  error('Not implemented yet')
+  
+else
+  
+  delete(obj.plot_window);
+
+end
+
+end
\ No newline at end of file
diff --git a/sc2/sc-viewer/viewer/+sc_viewer/@ScViewer/ScViewer.m b/sc2/sc-viewer/viewer/+sc_viewer/@ScViewer/ScViewer.m
index f18a267..3982239 100644
--- a/sc2/sc-viewer/viewer/+sc_viewer/@ScViewer/ScViewer.m
+++ b/sc2/sc-viewer/viewer/+sc_viewer/@ScViewer/ScViewer.m
@@ -7,6 +7,7 @@
     
     % User info text
     user_info
+    has_unsaved_changes = false
     
   end
   
diff --git a/sc2/sc-viewer/viewer/+sc_viewer/@ScViewer/set_experiment.m b/sc2/sc-viewer/viewer/+sc_viewer/@ScViewer/set_experiment.m
deleted file mode 100644
index 1cd3e0a..0000000
--- a/sc2/sc-viewer/viewer/+sc_viewer/@ScViewer/set_experiment.m
+++ /dev/null
@@ -1,23 +0,0 @@
-function set_experiment(obj, experiment)
-
-if ischar(experiment)
-
-  sc_settings.set_last_experiment(experiment);
-  experiment = load_experiment(experiment);
-  
-end
-
-obj.experiment = experiment;
-
-if isempty(experiment)
-  
-  obj.set_file([]);
-
-else
-  
-  file = get_set_val(obj.experiment.list, obj.file, 1);
-  obj.set_file(file);
-
-end
-
-end
diff --git a/sc2/sc-viewer/viewer/+sc_viewer/@ScViewer/set_file.m b/sc2/sc-viewer/viewer/+sc_viewer/@ScViewer/set_file.m
index f09a89c..7a9c199 100644
--- a/sc2/sc-viewer/viewer/+sc_viewer/@ScViewer/set_file.m
+++ b/sc2/sc-viewer/viewer/+sc_viewer/@ScViewer/set_file.m
@@ -6,6 +6,10 @@ function set_file(obj, file)
 if isempty(file)
   
   obj.set_sequence([]);
+  obj.set_signal1([]);
+  obj.set_signal2([]);
+  obj.set_trigger_parent([]);
+  
   return
 
 end
@@ -21,18 +25,22 @@ function set_file(obj, file)
   sequence = ScSequence(file, tag, tmin, tmax);
   file.add(sequence);
   
-elseif file.contains(obj.sequence)
-  
-  obj.set_sequence(obj.sequence);
-  
-elseif sc_contains(file.values('tag'), 'full')
-  
-  obj.set_sequence(obj.file.get('tag', 'full'));
-  
-else
+end
+
+obj.set_sequence(get_set_val(obj.file.list, obj.sequence, 'full'));
+
+signal1 = get_set_val(obj.file.signals.list, obj.signal1, 'patch');
+obj.set_signal1(signal1);
+
+if ~isempty(obj.signal2)
   
-  obj.set_sequence(obj.file.get(1));
+  signal2 = get_set_val(obj.file.signals.list, obj.signal2, 'patch2');
+  obj.set_signal2(signal2);
   
 end
 
+trigger_parents = obj.file.get_triggables();
+trigger_parent = get_set_val(trigger_parents, obj.trigger_parent);
+obj.set_trigger_parent(trigger_parent);
+
 end
diff --git a/sc2/sc-viewer/viewer/+sc_viewer/@ScViewer/set_sequence.m b/sc2/sc-viewer/viewer/+sc_viewer/@ScViewer/set_sequence.m
index e69de29..81620fc 100644
--- a/sc2/sc-viewer/viewer/+sc_viewer/@ScViewer/set_sequence.m
+++ b/sc2/sc-viewer/viewer/+sc_viewer/@ScViewer/set_sequence.m
@@ -0,0 +1,9 @@
+function set_sequence(obj, sequence)
+
+if isempty(obj.file)
+  obj.sequence = [];
+else
+  obj.sequence = get_item(obj.file.list, sequence);
+end
+
+end
\ No newline at end of file
diff --git a/sc2/sc-viewer/viewer/+sc_viewer/@ScViewer/set_trigger_parent.m b/sc2/sc-viewer/viewer/+sc_viewer/@ScViewer/set_trigger_parent.m
index 2452846..f0e9fd0 100644
--- a/sc2/sc-viewer/viewer/+sc_viewer/@ScViewer/set_trigger_parent.m
+++ b/sc2/sc-viewer/viewer/+sc_viewer/@ScViewer/set_trigger_parent.m
@@ -8,7 +8,7 @@ function set_trigger_parent(obj, val)
   
 else
   
-  trigger_tag = get_set_val(obj.trigger_parent.triggers.values('tag'), ...
+  trigger_tag = get_set_val(obj.trigger_parent.get_tags, ...
     obj.trigger_tag, 1);
   
 end
diff --git a/scripts/intra-analysis/intra_compare_amplitude_heights.m b/scripts/intra-analysis/intra_compare_amplitude_heights.m
new file mode 100644
index 0000000..fc040e3
--- /dev/null
+++ b/scripts/intra-analysis/intra_compare_amplitude_heights.m
@@ -0,0 +1,50 @@
+clear
+
+sc_settings.set_current_settings_tag(sc_settings.get_intra_analysis_tag());
+sc_debug.set_mode(true);
+
+intra_load_settings
+intra_load_constants
+
+reset_fig_indx();
+
+for i=1:length(neurons)
+  
+  signal = sc_load_signal(neurons(i));
+  
+  incr_fig_indx();
+  clf
+  
+  h1 = subplot(10, 1, 2:10);
+  hold on
+  
+  response_rate = nan(size(str_stims));
+  
+  for j=1:length(str_stims)
+    
+    amplitude = signal.amplitudes.get('tag', str_stims{j});
+    heights   = amplitude.height; 
+    
+    plot(j*ones(size(heights)), heights, 'k+');
+    response_rate(j) = length(heights) / amplitude.N;
+    
+  end
+  
+  set(gca, 'XTick', 1:length(str_stims), 'XTickLabel', str_stims, ...
+    'XTickLabelRotation', 270);
+  ylabel('EPSP amplitude [mV]')
+  grid on
+  
+  h2 = subplot(10, 1, 1);
+  bar(100*response_rate)
+  set(gca, 'XTick', []);
+  title(neurons(i).file_tag)
+  
+  linkaxes([h1 h2], 'x');
+  
+  xlim([0 (length(str_stims)+1)])
+  ylabel('Response rate %');
+  
+end
+  
+  
\ No newline at end of file
diff --git a/scripts/intra-analysis/intra_compare_avg_to_manual.m b/scripts/intra-analysis/intra_compare_avg_to_manual.m
new file mode 100644
index 0000000..90edc8c
--- /dev/null
+++ b/scripts/intra-analysis/intra_compare_avg_to_manual.m
@@ -0,0 +1,87 @@
+clear
+
+sc_settings.set_current_settings_tag(sc_settings.get_intra_analysis_tag());
+sc_debug.set_mode(true);
+
+intra_load_settings
+intra_load_constants
+
+reset_fig_indx();
+
+load intra_data.mat
+
+str_first_stims = arrayfun(@(x) x.stim_electrodes(1).tag, intra_patterns.patterns, 'UniformOutput', false);
+
+for i=1:length(neurons)
+  
+  neuron = neurons(i);
+  
+  signal = sc_load_signal(neuron);
+  
+  v = signal.get_v(true, false, false, false);
+  
+  incr_fig_indx();
+  clf
+  
+  for j=1:length(str_first_stims)
+    
+    sc_square_subplot(length(str_first_stims), j)
+    hold on
+    
+    first_amplitude = signal.amplitudes.get('tag', str_first_stims{j});
+    
+    [sweeps, times] = sc_get_sweeps(v, 0, first_amplitude.stimtimes, -.1, .5, signal.dt);
+    
+    [~, ind_zero] = min(abs(times));
+    
+    for kk=1:size(sweeps, 2)
+      
+      sweeps(:, kk) = sweeps(:, kk) - sweeps(ind_zero, kk);
+      %plot(times, sweeps(:, kk))
+      
+    end
+    
+    msweeps = mean(sweeps, 2);
+    plot(times, msweeps, 'LineWidth', 2)
+    
+    pattern = get_pattern(first_amplitude);
+    
+    str_pattern_stims = get_items(str_stims, @get_pattern, pattern);
+    
+    for k=1:length(str_pattern_stims)
+      
+      amplitude = signal.amplitudes.get('tag', str_pattern_stims{k});
+      
+      ind = cellfun(@(x) strcmp(str_pattern_stims{k}, x), {intra_patterns.stim_electrodes.tag});
+      offset = intra_patterns.stim_electrodes(ind).time;
+      [~, ind_offset] = min(abs(times - offset));
+      
+      x0 = offset + amplitude.latency;
+      y0 = zeros(size(x0));
+      
+      x1 = x0 + amplitude.width;
+      y1 = y0 + amplitude.height;
+      
+      ind = find(amplitude.valid_data);
+      
+%       for m=1:min(length(ind), 5)
+%         
+%         indx = times > x0(m) & times < x1(m);
+%         
+%         h = plot(times(indx), sweeps(indx, ind(m)));
+%         
+%         plot(x0(m), sweeps(ind_offset, ind(m))+ y0(m), '+', 'Color', get(h, 'Color'));
+%         plot(x1(m), sweeps(ind_offset, ind(m))+ y1(m), '+', 'Color', get(h, 'Color'));
+%       
+%       end
+      plot(x1, y1, '+', 'Tag', amplitude.tag)
+    
+    end
+    
+    title([neuron.file_tag ': ' pattern])
+    grid on
+    %add_legend()
+    
+  end
+  
+end
\ No newline at end of file
diff --git a/scripts/intra-analysis/intra_generate_figs.m b/scripts/intra-analysis/intra_generate_figs.m
index cdad33a..503ae80 100644
--- a/scripts/intra-analysis/intra_generate_figs.m
+++ b/scripts/intra-analysis/intra_generate_figs.m
@@ -11,7 +11,7 @@
 load intra_data.mat
 
 str_first_stims = arrayfun(@(x) x.stim_electrodes(1).tag, intra_patterns.patterns, 'UniformOutput', false);
-
+return
 stim_exists = false(size(str_first_stims));
 
 for i=1:length(str_first_stims)
diff --git a/scripts/paired-recordings/paired_compare_pairs.m b/scripts/paired-recordings/paired_compare_pairs.m
new file mode 100644
index 0000000..6ca5ba3
--- /dev/null
+++ b/scripts/paired-recordings/paired_compare_pairs.m
@@ -0,0 +1,23 @@
+function dist = paired_compare_pairs(neuron_pair_1, neuron_pair_2)
+
+f1 = get_f(neuron_pair_1);
+f2 = get_f(neuron_pair_2);
+
+%dist = min(sum(abs(f1-f2)), sum(abs(f1-f2(length(f2):-1:1))));
+dist = min(sqrt( sum( (f1-f2).^2 ) ), sqrt( sum( (f1-f2(length(f2):-1:1)).^2 )));
+
+end
+
+
+function f = get_f(neuron_pair)
+
+pretrigger  = -1;
+posttrigger = 1;
+kernelwidth = 1e-3;
+binwidth    = 1e-3;
+
+[t1, t2] = paired_get_neuron_spiketime(neuron_pair);
+f = sc_kernelfreq(t1, t2, pretrigger, posttrigger, 10*kernelwidth, binwidth);
+f = zscore(f);
+
+end
diff --git a/scripts/paired-recordings/paired_compare_triplets.m b/scripts/paired-recordings/paired_compare_triplets.m
new file mode 100644
index 0000000..e64891c
--- /dev/null
+++ b/scripts/paired-recordings/paired_compare_triplets.m
@@ -0,0 +1,120 @@
+clear
+paired_setup
+
+reset_fig_indx()
+
+pretrigger  = -1;
+posttrigger = 1;
+kernelwidth = 1e-3;
+binwidth    = 1e-3;
+
+file_tags = unique({ec_neurons.file_tag});
+
+triplet_file_tags = file_tags(arrayfun(@(y) nnz(arrayfun(@(x) strcmp(x.file_tag, y), ec_neurons))>1, file_tags));
+
+triplets_list = {};
+
+for i=1:length(triplet_file_tags)
+  
+  triplets = ec_neurons(arrayfun(@(x) strcmp(x.file_tag, triplet_file_tags{i}), ec_neurons));
+    
+  triplets_list = add_to_list(triplets_list, triplets);
+  
+  incr_fig_indx()
+  clf
+  
+  for j=1:length(triplets)  
+    
+    tmp_triplet_1 = triplets(j);
+    [t1, t2] = paired_get_neuron_spiketime(tmp_triplet_1);
+    
+    sc_square_subplot(2*length(triplets), 2*j-1);
+    hold on
+    sc_kernelhist(t1, t2, pretrigger, posttrigger, kernelwidth, binwidth);
+    [~, ~, h_plot] = sc_kernelhist(t1, t2, pretrigger, posttrigger, 10*kernelwidth, binwidth);
+    set(h_plot, 'LineWidth', 2);
+    grid on
+    title([tmp_triplet_1.file_tag ': ' tmp_triplet_1.template_tag{1} ' - ' tmp_triplet_1.template_tag{2}])
+    
+    sc_square_subplot(2*length(triplets), 2*j);
+    hold on
+    sc_kernelhist(t2, t1, pretrigger, posttrigger, kernelwidth, binwidth);
+    [~, ~, h_plot] = sc_kernelhist(t2, t1, pretrigger, posttrigger, 10*kernelwidth, binwidth);
+    set(h_plot, 'LineWidth', 2);
+    grid on
+    
+  end
+  
+end
+
+ind1 = 0;
+
+labels = {};
+
+clear dist
+
+avg_dist_same = [];
+avg_dist_different = [];
+
+for i=1:length(triplets_list)
+  
+  sc_debug.print(i, length(triplets_list));
+  
+  tmp_triplet_list_1 = triplets_list{i};
+  
+  for j=1:length(tmp_triplet_list_1)
+    
+    tmp_triplet_1 = tmp_triplet_list_1(j);
+    ind1 = ind1 + 1;
+    ind2 = 0;
+    labels = add_to_list(labels, tmp_triplet_1.file_tag);
+    
+    for k=1:length(triplets_list)
+  
+      tmp_triplet_list_2 = triplets_list{k};
+      
+      for m=1:length(tmp_triplet_list_2)
+        
+        tmp_triplet_2 = tmp_triplet_list_2(m);
+        ind2 = ind2+1;
+        
+        d = paired_compare_pairs(tmp_triplet_1, tmp_triplet_2);
+        dist(ind1, ind2) = d;
+        
+        if length(tmp_triplet_list_1) == length(tmp_triplet_list_2) && ...
+          all(tmp_triplet_list_1 == tmp_triplet_list_2)
+        
+          if ind1 ~= ind2
+            avg_dist_same = add_to_list(avg_dist_same, d);
+          end
+        else
+          avg_dist_different = add_to_list(avg_dist_different, d);
+        end
+        
+      end
+      
+    end
+    
+  end
+  
+end
+        
+incr_fig_indx();
+clf
+fill_matrix(dist);
+colorbar
+set(gca, 'XTick', (1:length(labels)), 'XTickLabel', labels, ...
+  'YTick', (1:length(labels)), 'YTickLabel', labels, ...
+  'XTickLabelRotation', 270);
+
+incr_fig_indx
+clf
+plot(avg_dist_same, ones(size(avg_dist_same)), '+')
+hold on
+plot(avg_dist_different, 2*ones(size(avg_dist_different)), '+')
+ylim([0 3])
+plot(mean(avg_dist_different), 2, 'o')
+plot(mean(avg_dist_same), 1, 'o')
+plot(median(avg_dist_different), 2, '^')
+plot(median(avg_dist_same), 1, '^')
+