diff --git a/.gitignore b/.gitignore
index 8298fba1..8ed29ac6 100644
--- a/.gitignore
+++ b/.gitignore
@@ -95,3 +95,13 @@ arm64
 /examples/test/images/c302_C1_Oscillator.net.nml
 /examples/test/images/LEMS_c302_C1_Oscillator.xml
 /c302/VarshneyDataReader2.py
+/
+/examples/test/images/LEMS_c302_C1_Full.xml
+/examples/test/images/LEMS_c302_C1_Muscles.xml
+/examples/test/images/LEMS_c302_C1_Social.xml
+/examples/test/images/LEMS_c302_C1_Syns.xml
+/examples/test/images/c302_C1_Full.net.nml
+/examples/test/images/c302_C1_Muscles.net.nml
+/examples/test/images/c302_C1_Pharyngeal.net.nml
+/examples/test/images/c302_C1_Social.net.nml
+/examples/test/images/c302_C1_Syns.net.nml
diff --git a/c302/Cook2019DataReader.py b/c302/Cook2019DataReader.py
index 6ae3b34a..dc7cf361 100644
--- a/c302/Cook2019DataReader.py
+++ b/c302/Cook2019DataReader.py
@@ -47,7 +47,9 @@ def get_synclass(cell, syntype):
             return "GABA"
         return "Acetylcholine"
 
-class Cook2019DataReaderReader():
+class Cook2019DataReader():
+
+    verbose = False
 
     def __init__(self):
 
@@ -69,12 +71,12 @@ def __init__(self):
             for i in pre_range[conn_type]:
                 self.pre_cells[conn_type].append(sheet['C%i'%i].value)
 
-            print(' - Pre cells for %s (%i):\n%s'%(conn_type, len(self.pre_cells[conn_type]), self.pre_cells[conn_type]))
+            if self.verbose: print(' - Pre cells for %s (%i):\n%s'%(conn_type, len(self.pre_cells[conn_type]), self.pre_cells[conn_type]))
 
             for i in post_range[conn_type]:
                 self.post_cells[conn_type].append(sheet.cell(row=3, column=i).value)
 
-            print(' - Post cells for %s (%i):\n%s'%(conn_type, len(self.post_cells[conn_type]), self.post_cells[conn_type]))
+            if self.verbose: print(' - Post cells for %s (%i):\n%s'%(conn_type, len(self.post_cells[conn_type]), self.post_cells[conn_type]))
 
             self.conn_nums[conn_type] = np.zeros([len(self.pre_cells[conn_type]),len(self.post_cells[conn_type])], dtype=int)
 
@@ -87,8 +89,7 @@ def __init__(self):
                     if val is not None:
                         self.conn_nums[conn_type][i,j] = int(val)
 
-            print()
-            print(' - Conns for %s (%s):\n%s'%(conn_type, self.conn_nums[conn_type].shape, self.conn_nums[conn_type]))
+            if self.verbose: print(' - Conns for %s (%s):\n%s'%(conn_type, self.conn_nums[conn_type].shape, self.conn_nums[conn_type]))
 
 
 
@@ -167,14 +168,14 @@ def read_muscle_data(self):
                 elif is_body_wall_muscle(pre) and pre not in muscles:
                     muscles.append(pre)
                 if post not in muscles:
-                    muscles.append(post)'''
+                    muscles.append(post)''' 
 
         return neurons, muscles, conns
 
 
 def main():
 
-    cdr = Cook2019DataReaderReader()
+    cdr = Cook2019DataReader()
     read_data = cdr.read_data
     read_muscle_data = cdr.read_muscle_data
     
diff --git a/c302/Cook2019HermReader.py b/c302/Cook2019HermReader.py
new file mode 100644
index 00000000..9ccd96dd
--- /dev/null
+++ b/c302/Cook2019HermReader.py
@@ -0,0 +1,19 @@
+# Temporary class to allow this to be used in comparison notebook. 
+# Should be tidied up.
+
+from c302.Cook2019DataReader import Cook2019DataReader
+
+from c302.ConnectomeReader import analyse_connections
+
+cdr = Cook2019DataReader()
+read_data = cdr.read_data
+read_muscle_data = cdr.read_muscle_data
+
+def main1():
+    cells, neuron_conns = read_data(include_nonconnected_cells=True)
+    neurons2muscles, muscles, muscle_conns = read_muscle_data()
+    analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_conns)
+
+
+if __name__ == '__main__':
+    main1()
\ No newline at end of file
diff --git a/c302/__init__.py b/c302/__init__.py
index 31c6f4df..581c08b8 100755
--- a/c302/__init__.py
+++ b/c302/__init__.py
@@ -465,7 +465,7 @@ def _get_cell_info(bnd, cells):
     for name in fixed_up_names:
         cell = next(ctx(Cell).query(name=name).load(), None)
         if cell is None:
-            print_("No matching cell for %s" % name)
+            #print_("No matching cell for %s" % name)
             continue
 
         normalized_name = cell.name()
diff --git a/c302/c302_utils.py b/c302/c302_utils.py
index 784d321e..7cac4aa7 100644
--- a/c302/c302_utils.py
+++ b/c302/c302_utils.py
@@ -577,6 +577,8 @@ def generate_conn_matrix(nml_doc, save_fig_dir=None, verbose=False, figsize=defa
     configs = ['c302_C0_Muscles.net.nml']
     configs = ['c302_C0_Syns.net.nml', 'c302_C0_Social.net.nml','c302_C0_Muscles.net.nml','c302_C0_Pharyngeal.net.nml','c302_C0_Oscillator.net.nml','c302_C0_Full.net.nml']
     
+    figsize=(6.4,4.8)
+
     if '-phar' in sys.argv:
 
         configs = ['c302_C0_Pharyngeal.net.nml']
@@ -585,11 +587,21 @@ def generate_conn_matrix(nml_doc, save_fig_dir=None, verbose=False, figsize=defa
 
         configs = ['c302_C1_Oscillator.net.nml']
 
+    elif '-musc' in sys.argv:
+
+        configs = ['c302_C1_Muscles.net.nml']
+        figsize=(10,10)
+
+    elif '-full' in sys.argv:
+
+        configs = ['c302_C1_Full.net.nml']
+        figsize=(10,10)
+
     for c in configs:
 
         nml_doc = read_neuroml2_file('examples/%s'%c)
 
-        generate_conn_matrix(nml_doc, save_fig_dir='./examples/summary/images', figsize=(6.4,4.8))
+        generate_conn_matrix(nml_doc, save_fig_dir='./examples/summary/images', figsize=figsize)
 
     if not '-nogui' in sys.argv:
         plt.show()
diff --git a/examples/test/Comparison.ipynb b/examples/test/Comparison.ipynb
index 22a63a3a..21db5a81 100644
--- a/examples/test/Comparison.ipynb
+++ b/examples/test/Comparison.ipynb
@@ -75,6 +75,11 @@
      "text": [
       "c302      >>>  Initialising WormNeuroAtlasReader\n",
       "\n",
+      "****** Importing dataset Cook2019Herm using c302.Cook2019HermReader ******\n",
+      "c302      >>>  Opened the Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/SI 5 Connectome adjacency matrices.xlsx\n",
+      "Looking at sheet: hermaphrodite chemical\n",
+      "Looking at sheet: herm gap jn symmetric\n",
+      "\n",
       "Finished loading all the data from the readers!\n"
      ]
     }
@@ -107,6 +112,7 @@
     "           \"Witvliet1\": \"c302.WitvlietDataReader1\",\n",
     "           \"Witvliet2\": \"c302.WitvlietDataReader2\",\n",
     "           \"WormNeuroAtlas\": \"c302.WormNeuroAtlasReader\",\n",
+    "           \"Cook2019Herm\": \"c302.Cook2019HermReader\",\n",
     "          }\n",
     "\n",
     "def shorten_neurotransmitter(nt):\n",
@@ -194,6 +200,7 @@
        "      <th>Witvliet1</th>\n",
        "      <th>Witvliet2</th>\n",
        "      <th>WormNeuroAtlas</th>\n",
+       "      <th>Cook2019Herm</th>\n",
        "    </tr>\n",
        "  </thead>\n",
        "  <tbody>\n",
@@ -210,6 +217,7 @@
        "      <td>181</td>\n",
        "      <td>180</td>\n",
        "      <td>300</td>\n",
+       "      <td>302</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <td>Missing neurons</td>\n",
@@ -224,6 +232,7 @@
        "      <td>121</td>\n",
        "      <td>122</td>\n",
        "      <td>2</td>\n",
+       "      <td>0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <td>Non neurons</td>\n",
@@ -238,6 +247,7 @@
        "      <td>9</td>\n",
        "      <td>7</td>\n",
        "      <td>0</td>\n",
+       "      <td>96</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <td>Num muscles</td>\n",
@@ -252,6 +262,7 @@
        "      <td>32</td>\n",
        "      <td>32</td>\n",
        "      <td>0</td>\n",
+       "      <td>0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <td>Num N->N conns</td>\n",
@@ -266,6 +277,7 @@
        "      <td>2251</td>\n",
        "      <td>2274</td>\n",
        "      <td>5701</td>\n",
+       "      <td>6577</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <td>Num N with ->M</td>\n",
@@ -280,6 +292,7 @@
        "      <td>58</td>\n",
        "      <td>47</td>\n",
        "      <td>0</td>\n",
+       "      <td>0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <td>Num N->M conns</td>\n",
@@ -294,6 +307,7 @@
        "      <td>230</td>\n",
        "      <td>216</td>\n",
        "      <td>0</td>\n",
+       "      <td>0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <td>N->N neurotrans.</td>\n",
@@ -308,6 +322,7 @@
        "      <td>Gen_CS (1979)<br/>Gen_GJ (272)<br/></td>\n",
        "      <td>Gen_CS (1970)<br/>Gen_GJ (304)<br/></td>\n",
        "      <td>ACh (2017)<br/>GABA (631)<br/>Gen_CS (431)<br/>Gen_GJ (1650)<br/>Glu (972)<br/></td>\n",
+       "      <td>ACh (3859)<br/>GABA (64)<br/>Gen_GJ (2654)<br/></td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <td>N->M neurotrans.</td>\n",
@@ -322,6 +337,7 @@
        "      <td>Gen_CS (230)<br/></td>\n",
        "      <td>Gen_CS (216)<br/></td>\n",
        "      <td></td>\n",
+       "      <td></td>\n",
        "    </tr>\n",
        "  </tbody>\n",
        "</table>"
@@ -359,7 +375,166 @@
      "output_type": "stream",
      "text": [
       "\n",
-      "=== Generating using reader SpreadsheetDataReader\n",
+      "=== Generating using reader c302.SpreadsheetDataReader (SSData)\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C1\n",
+      "c302      >>>  Opened Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/CElegansNeuronTables.xls\n",
+      "c302      >>>  Opened Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/CElegansNeuronTables.xls\n",
+      "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Social.net.nml\n",
+      "c302      >>>  (Re)written network file to: images/c302_C1_Social.net.nml\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Social/SSData_exc_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Social/SSData_elec_neurons_neurons.png\n",
+      "\n",
+      "=== Generating using reader c302.UpdatedSpreadsheetDataReader (UpdSSData)\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C1\n",
+      "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/herm_full_edgelist.csv\n",
+      "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/herm_full_edgelist.csv\n",
+      "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Social.net.nml\n",
+      "c302      >>>  (Re)written network file to: images/c302_C1_Social.net.nml\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Social/UpdSSData_exc_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Social/UpdSSData_elec_neurons_neurons.png\n",
+      "\n",
+      "=== Generating using reader c302.UpdatedSpreadsheetDataReader2 (UpdSSData2)\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C1\n",
+      "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/herm_full_edgelist_MODIFIED.csv\n",
+      "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/herm_full_edgelist_MODIFIED.csv\n",
+      "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Social.net.nml\n",
+      "c302      >>>  (Re)written network file to: images/c302_C1_Social.net.nml\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Social/UpdSSData2_exc_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Social/UpdSSData2_elec_neurons_neurons.png\n",
+      "\n",
+      "=== Generating using reader c302.OpenWormReader (OpenWorm)\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C1\n",
+      "c302      >>>  Initialising OpenWormReader\n",
+      "c302      >>>  Total cells 302 (300 with connections)\n",
+      "c302      >>>  Total connections found 5805 \n",
+      "c302      >>>  Total cells 397 (254 with connections)\n",
+      "c302      >>>  Total connections found 926 \n",
+      "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Social.net.nml\n",
+      "c302      >>>  (Re)written network file to: images/c302_C1_Social.net.nml\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Social/OpenWorm_exc_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Social/OpenWorm_elec_neurons_neurons.png\n",
+      "\n",
+      "=== Generating using reader c302.White_A (White_A)\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C1\n",
+      "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_A.csv\n",
+      "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_A.csv\n",
+      "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Social.net.nml\n",
+      "c302      >>>  (Re)written network file to: images/c302_C1_Social.net.nml\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Social/White_A_exc_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Social/White_A_elec_neurons_neurons.png\n",
+      "\n",
+      "=== Generating using reader c302.White_L4 (White_L4)\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C1\n",
+      "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_L4.csv\n",
+      "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_L4.csv\n",
+      "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Social.net.nml\n",
+      "c302      >>>  (Re)written network file to: images/c302_C1_Social.net.nml\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Social/White_L4_exc_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Social/White_L4_elec_neurons_neurons.png\n",
+      "\n",
+      "=== Generating using reader c302.White_whole (White_whole)\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C1\n",
+      "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_whole.csv\n",
+      "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_whole.csv\n",
+      "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Social.net.nml\n",
+      "c302      >>>  (Re)written network file to: images/c302_C1_Social.net.nml\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Social/White_whole_exc_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Social/White_whole_elec_neurons_neurons.png\n",
+      "\n",
+      "=== Generating using reader c302.VarshneyDataReader (Varshney)\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C1\n",
+      "c302      >>>  Opened the Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/NeuronConnectFormatted.xlsx\n",
+      "c302      >>>  Opened Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/NeuronConnectFormatted.xlsx\n",
+      "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Social.net.nml\n",
+      "c302      >>>  (Re)written network file to: images/c302_C1_Social.net.nml\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Social/VarshneyData_exc_to_neurons.png\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/c302_utils.py:369: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`). Consider using `matplotlib.pyplot.close()`.\n",
+      "  fig, ax = plt.subplots(figsize=figsize)\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "c302      >>>  Saving connectivity figure to: ./images/Social/VarshneyData_elec_neurons_neurons.png\n",
+      "\n",
+      "=== Generating using reader c302.WitvlietDataReader1 (Witvliet1)\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C1\n",
+      "c302      >>>  Opened the Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/witvliet_2020_7.xlsx\n",
+      "c302      >>>  Opened Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/witvliet_2020_7.xlsx\n",
+      "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Social.net.nml\n",
+      "c302      >>>  (Re)written network file to: images/c302_C1_Social.net.nml\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Social/WitvlietData1_exc_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Social/WitvlietData1_elec_neurons_neurons.png\n",
+      "\n",
+      "=== Generating using reader c302.WitvlietDataReader2 (Witvliet2)\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C1\n",
+      "c302      >>>  Opened the Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/witvliet_2020_8.xlsx\n",
+      "c302      >>>  Opened Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/witvliet_2020_8.xlsx\n",
+      "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Social.net.nml\n",
+      "c302      >>>  (Re)written network file to: images/c302_C1_Social.net.nml\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Social/WitvlietData2_exc_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Social/WitvlietData2_elec_neurons_neurons.png\n",
+      "\n",
+      "=== Generating using reader c302.WormNeuroAtlasReader (WormNeuroAtlas)\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C1\n",
+      "c302      >>>  Initialising WormNeuroAtlasReader\n",
+      "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Social.net.nml\n",
+      "c302      >>>  (Re)written network file to: images/c302_C1_Social.net.nml\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Social/WormNeuroAtlas_exc_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Social/WormNeuroAtlas_elec_neurons_neurons.png\n",
+      "\n",
+      "=== Generating using reader c302.Cook2019HermReader (Cook2019Herm)\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C1\n",
+      "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Social.net.nml\n",
+      "c302      >>>  (Re)written network file to: images/c302_C1_Social.net.nml\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Social/Cook2019Herm_exc_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Social/Cook2019Herm_elec_neurons_neurons.png\n",
+      "Finished generation of images!\n",
+      "\n",
+      "=== Generating using reader c302.SpreadsheetDataReader (SSData)\n",
       "c302      >>>  Set default parameters for C\n",
       "c302      >>>  Set default parameters for C\n",
       "c302      >>>  Set default parameters for C\n",
@@ -367,11 +542,11 @@
       "c302      >>>  Opened Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/CElegansNeuronTables.xls\n",
       "c302      >>>  Opened Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/CElegansNeuronTables.xls\n",
       "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Oscillator.net.nml\n",
-      "c302      >>>  Saving connectivity figure to: ./images/SSData_exc_to_neurons.png\n",
-      "c302      >>>  Saving connectivity figure to: ./images/SSData_inh_to_neurons.png\n",
-      "c302      >>>  Saving connectivity figure to: ./images/SSData_elec_neurons_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Oscillator/SSData_exc_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Oscillator/SSData_inh_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Oscillator/SSData_elec_neurons_neurons.png\n",
       "\n",
-      "=== Generating using reader UpdatedSpreadsheetDataReader\n",
+      "=== Generating using reader c302.UpdatedSpreadsheetDataReader (UpdSSData)\n",
       "c302      >>>  Set default parameters for C\n",
       "c302      >>>  Set default parameters for C\n",
       "c302      >>>  Set default parameters for C\n",
@@ -379,11 +554,11 @@
       "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/herm_full_edgelist.csv\n",
       "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/herm_full_edgelist.csv\n",
       "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Oscillator.net.nml\n",
-      "c302      >>>  Saving connectivity figure to: ./images/UpdSSData_exc_to_neurons.png\n",
-      "c302      >>>  Saving connectivity figure to: ./images/UpdSSData_inh_to_neurons.png\n",
-      "c302      >>>  Saving connectivity figure to: ./images/UpdSSData_elec_neurons_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Oscillator/UpdSSData_exc_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Oscillator/UpdSSData_inh_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Oscillator/UpdSSData_elec_neurons_neurons.png\n",
       "\n",
-      "=== Generating using reader UpdatedSpreadsheetDataReader2\n",
+      "=== Generating using reader c302.UpdatedSpreadsheetDataReader2 (UpdSSData2)\n",
       "c302      >>>  Set default parameters for C\n",
       "c302      >>>  Set default parameters for C\n",
       "c302      >>>  Set default parameters for C\n",
@@ -391,11 +566,11 @@
       "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/herm_full_edgelist_MODIFIED.csv\n",
       "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/herm_full_edgelist_MODIFIED.csv\n",
       "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Oscillator.net.nml\n",
-      "c302      >>>  Saving connectivity figure to: ./images/UpdSSData2_exc_to_neurons.png\n",
-      "c302      >>>  Saving connectivity figure to: ./images/UpdSSData2_inh_to_neurons.png\n",
-      "c302      >>>  Saving connectivity figure to: ./images/UpdSSData2_elec_neurons_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Oscillator/UpdSSData2_exc_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Oscillator/UpdSSData2_inh_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Oscillator/UpdSSData2_elec_neurons_neurons.png\n",
       "\n",
-      "=== Generating using reader OpenWormReader\n",
+      "=== Generating using reader c302.OpenWormReader (OpenWorm)\n",
       "c302      >>>  Set default parameters for C\n",
       "c302      >>>  Set default parameters for C\n",
       "c302      >>>  Set default parameters for C\n",
@@ -406,50 +581,43 @@
       "c302      >>>  Total cells 397 (254 with connections)\n",
       "c302      >>>  Total connections found 926 \n",
       "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Oscillator.net.nml\n",
-      "c302      >>>  Saving connectivity figure to: ./images/OpenWorm_exc_to_neurons.png\n",
-      "c302      >>>  Saving connectivity figure to: ./images/OpenWorm_inh_to_neurons.png\n",
-      "c302      >>>  Saving connectivity figure to: ./images/OpenWorm_elec_neurons_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Oscillator/OpenWorm_exc_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Oscillator/OpenWorm_inh_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Oscillator/OpenWorm_elec_neurons_neurons.png\n",
       "\n",
-      "=== Generating using reader White_A\n",
+      "=== Generating using reader c302.White_A (White_A)\n",
       "c302      >>>  Set default parameters for C\n",
       "c302      >>>  Set default parameters for C\n",
       "c302      >>>  Set default parameters for C\n",
       "c302      >>>  Set default parameters for C1\n",
       "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_A.csv\n",
-      "c302      >>>  No matching cell for CEPshVL\n",
-      "c302      >>>  No matching cell for CEPshDR\n",
-      "c302      >>>  No matching cell for CEPshVR\n",
       "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_A.csv\n",
       "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Oscillator.net.nml\n",
-      "c302      >>>  Saving connectivity figure to: ./images/White_A_elec_neurons_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Oscillator/White_A_elec_neurons_neurons.png\n",
       "\n",
-      "=== Generating using reader White_L4\n",
+      "=== Generating using reader c302.White_L4 (White_L4)\n",
       "c302      >>>  Set default parameters for C\n",
       "c302      >>>  Set default parameters for C\n",
       "c302      >>>  Set default parameters for C\n",
       "c302      >>>  Set default parameters for C1\n",
       "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_L4.csv\n",
-      "c302      >>>  No matching cell for CEPshVL\n",
-      "c302      >>>  No matching cell for CEPshVR\n",
       "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_L4.csv\n",
       "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Oscillator.net.nml\n",
-      "c302      >>>  Saving connectivity figure to: ./images/White_L4_elec_neurons_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Oscillator/White_L4_elec_neurons_neurons.png\n",
       "\n",
-      "=== Generating using reader White_whole\n",
+      "=== Generating using reader c302.White_whole (White_whole)\n",
       "c302      >>>  Set default parameters for C\n",
       "c302      >>>  Set default parameters for C\n",
       "c302      >>>  Set default parameters for C\n",
       "c302      >>>  Set default parameters for C1\n",
       "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_whole.csv\n",
-      "c302      >>>  No matching cell for pm1\n",
-      "c302      >>>  No matching cell for pm4\n",
       "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_whole.csv\n",
       "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Oscillator.net.nml\n",
-      "c302      >>>  Saving connectivity figure to: ./images/White_whole_exc_to_neurons.png\n",
-      "c302      >>>  Saving connectivity figure to: ./images/White_whole_inh_to_neurons.png\n",
-      "c302      >>>  Saving connectivity figure to: ./images/White_whole_elec_neurons_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Oscillator/White_whole_exc_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Oscillator/White_whole_inh_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Oscillator/White_whole_elec_neurons_neurons.png\n",
       "\n",
-      "=== Generating using reader VarshneyDataReader\n",
+      "=== Generating using reader c302.VarshneyDataReader (Varshney)\n",
       "c302      >>>  Set default parameters for C\n",
       "c302      >>>  Set default parameters for C\n",
       "c302      >>>  Set default parameters for C\n",
@@ -457,47 +625,172 @@
       "c302      >>>  Opened the Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/NeuronConnectFormatted.xlsx\n",
       "c302      >>>  Opened Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/NeuronConnectFormatted.xlsx\n",
       "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Oscillator.net.nml\n",
-      "c302      >>>  Saving connectivity figure to: ./images/VarshneyData_exc_to_neurons.png\n",
-      "c302      >>>  Saving connectivity figure to: ./images/VarshneyData_elec_neurons_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Oscillator/VarshneyData_exc_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Oscillator/VarshneyData_elec_neurons_neurons.png\n",
       "\n",
-      "=== Generating using reader WitvlietDataReader1\n",
+      "=== Generating using reader c302.WitvlietDataReader1 (Witvliet1)\n",
       "c302      >>>  Set default parameters for C\n",
       "c302      >>>  Set default parameters for C\n",
       "c302      >>>  Set default parameters for C\n",
       "c302      >>>  Set default parameters for C1\n",
       "c302      >>>  Opened the Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/witvliet_2020_7.xlsx\n",
-      "c302      >>>  No matching cell for CEPshVL\n",
-      "c302      >>>  No matching cell for CEPshDL\n",
-      "c302      >>>  No matching cell for CEPshDR\n",
-      "c302      >>>  No matching cell for CEPshVR\n",
       "c302      >>>  Opened Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/witvliet_2020_7.xlsx\n",
       "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Oscillator.net.nml\n",
-      "c302      >>>  Saving connectivity figure to: ./images/WitvlietData1_elec_neurons_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Oscillator/WitvlietData1_elec_neurons_neurons.png\n",
       "\n",
-      "=== Generating using reader WitvlietDataReader2\n",
+      "=== Generating using reader c302.WitvlietDataReader2 (Witvliet2)\n",
       "c302      >>>  Set default parameters for C\n",
       "c302      >>>  Set default parameters for C\n",
       "c302      >>>  Set default parameters for C\n",
       "c302      >>>  Set default parameters for C1\n",
       "c302      >>>  Opened the Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/witvliet_2020_8.xlsx\n",
-      "c302      >>>  No matching cell for CEPshVL\n",
-      "c302      >>>  No matching cell for CEPshDL\n",
-      "c302      >>>  No matching cell for CEPshDR\n",
-      "c302      >>>  No matching cell for CEPshVR\n",
       "c302      >>>  Opened Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/witvliet_2020_8.xlsx\n",
       "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Oscillator.net.nml\n",
-      "c302      >>>  Saving connectivity figure to: ./images/WitvlietData2_elec_neurons_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Oscillator/WitvlietData2_elec_neurons_neurons.png\n",
       "\n",
-      "=== Generating using reader WormNeuroAtlasReader\n",
+      "=== Generating using reader c302.WormNeuroAtlasReader (WormNeuroAtlas)\n",
       "c302      >>>  Set default parameters for C\n",
       "c302      >>>  Set default parameters for C\n",
       "c302      >>>  Set default parameters for C\n",
       "c302      >>>  Set default parameters for C1\n",
       "c302      >>>  Initialising WormNeuroAtlasReader\n",
       "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Oscillator.net.nml\n",
-      "c302      >>>  Saving connectivity figure to: ./images/WormNeuroAtlas_exc_to_neurons.png\n",
-      "c302      >>>  Saving connectivity figure to: ./images/WormNeuroAtlas_inh_to_neurons.png\n",
-      "c302      >>>  Saving connectivity figure to: ./images/WormNeuroAtlas_elec_neurons_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Oscillator/WormNeuroAtlas_exc_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Oscillator/WormNeuroAtlas_inh_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Oscillator/WormNeuroAtlas_elec_neurons_neurons.png\n",
+      "\n",
+      "=== Generating using reader c302.Cook2019HermReader (Cook2019Herm)\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C1\n",
+      "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Oscillator.net.nml\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Oscillator/Cook2019Herm_exc_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Oscillator/Cook2019Herm_inh_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Oscillator/Cook2019Herm_elec_neurons_neurons.png\n",
+      "Finished generation of images!\n",
+      "\n",
+      "=== Generating using reader c302.SpreadsheetDataReader (SSData)\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C1\n",
+      "c302      >>>  Opened Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/CElegansNeuronTables.xls\n",
+      "c302      >>>  Opened Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/CElegansNeuronTables.xls\n",
+      "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Pharyngeal.net.nml\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Pharyngeal/SSData_exc_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Pharyngeal/SSData_elec_neurons_neurons.png\n",
+      "\n",
+      "=== Generating using reader c302.UpdatedSpreadsheetDataReader (UpdSSData)\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C1\n",
+      "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/herm_full_edgelist.csv\n",
+      "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/herm_full_edgelist.csv\n",
+      "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Pharyngeal.net.nml\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Pharyngeal/UpdSSData_exc_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Pharyngeal/UpdSSData_elec_neurons_neurons.png\n",
+      "\n",
+      "=== Generating using reader c302.UpdatedSpreadsheetDataReader2 (UpdSSData2)\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C1\n",
+      "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/herm_full_edgelist_MODIFIED.csv\n",
+      "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/herm_full_edgelist_MODIFIED.csv\n",
+      "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Pharyngeal.net.nml\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Pharyngeal/UpdSSData2_exc_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Pharyngeal/UpdSSData2_elec_neurons_neurons.png\n",
+      "\n",
+      "=== Generating using reader c302.OpenWormReader (OpenWorm)\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C1\n",
+      "c302      >>>  Initialising OpenWormReader\n",
+      "c302      >>>  Total cells 302 (300 with connections)\n",
+      "c302      >>>  Total connections found 5805 \n",
+      "c302      >>>  Total cells 397 (254 with connections)\n",
+      "c302      >>>  Total connections found 926 \n",
+      "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Pharyngeal.net.nml\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Pharyngeal/OpenWorm_exc_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Pharyngeal/OpenWorm_elec_neurons_neurons.png\n",
+      "\n",
+      "=== Generating using reader c302.White_A (White_A)\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C1\n",
+      "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_A.csv\n",
+      "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_A.csv\n",
+      "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Pharyngeal.net.nml\n",
+      "\n",
+      "=== Generating using reader c302.White_L4 (White_L4)\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C1\n",
+      "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_L4.csv\n",
+      "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_L4.csv\n",
+      "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Pharyngeal.net.nml\n",
+      "\n",
+      "=== Generating using reader c302.White_whole (White_whole)\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C1\n",
+      "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_whole.csv\n",
+      "c302      >>>  Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_whole.csv\n",
+      "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Pharyngeal.net.nml\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Pharyngeal/White_whole_exc_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Pharyngeal/White_whole_elec_neurons_neurons.png\n",
+      "\n",
+      "=== Generating using reader c302.VarshneyDataReader (Varshney)\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C1\n",
+      "c302      >>>  Opened the Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/NeuronConnectFormatted.xlsx\n",
+      "c302      >>>  Opened Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/NeuronConnectFormatted.xlsx\n",
+      "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Pharyngeal.net.nml\n",
+      "\n",
+      "=== Generating using reader c302.WitvlietDataReader1 (Witvliet1)\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C1\n",
+      "c302      >>>  Opened the Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/witvliet_2020_7.xlsx\n",
+      "c302      >>>  Opened Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/witvliet_2020_7.xlsx\n",
+      "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Pharyngeal.net.nml\n",
+      "\n",
+      "=== Generating using reader c302.WitvlietDataReader2 (Witvliet2)\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C1\n",
+      "c302      >>>  Opened the Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/witvliet_2020_8.xlsx\n",
+      "c302      >>>  Opened Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/witvliet_2020_8.xlsx\n",
+      "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Pharyngeal.net.nml\n",
+      "\n",
+      "=== Generating using reader c302.WormNeuroAtlasReader (WormNeuroAtlas)\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C1\n",
+      "c302      >>>  Initialising WormNeuroAtlasReader\n",
+      "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Pharyngeal.net.nml\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Pharyngeal/WormNeuroAtlas_exc_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Pharyngeal/WormNeuroAtlas_elec_neurons_neurons.png\n",
+      "\n",
+      "=== Generating using reader c302.Cook2019HermReader (Cook2019Herm)\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C\n",
+      "c302      >>>  Set default parameters for C1\n",
+      "c302      >>>  Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Pharyngeal.net.nml\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Pharyngeal/Cook2019Herm_exc_to_neurons.png\n",
+      "c302      >>>  Saving connectivity figure to: ./images/Pharyngeal/Cook2019Herm_elec_neurons_neurons.png\n",
       "Finished generation of images!\n"
      ]
     }
@@ -508,32 +801,51 @@
     "    \n",
     "parameter_set = 'C1'\n",
     "\n",
-    "from c302.c302_Oscillator import setup\n",
-    "from c302.c302_utils import generate_conn_matrix\n",
+    "configs = ['Social','Oscillator', 'Pharyngeal']\n",
     "\n",
-    "import matplotlib.pyplot as plt\n",
     "\n",
-    "plt.ioff()\n",
+    "import importlib as IM\n",
     "\n",
-    "for reader_module in readers.values():\n",
+    "for config in configs:\n",
     "    \n",
-    "    reader = reader_module[5:]\n",
+    "    with open('%s.md'%config, 'w') as f:\n",
     "        \n",
-    "    print(\"\\n=== Generating using reader %s\"%reader)\n",
-    "    setup(parameter_set, \n",
-    "          generate=True, \n",
-    "          target_directory='images',\n",
-    "          data_reader=reader,\n",
-    "          verbose=False)\n",
+    "        f.write('|EXC|INH|GJ|\\n')\n",
+    "        f.write('|-|-|-|\\n')\n",
     "\n",
-    "    nml_filename = 'c302_%s_Oscillator.net.nml'%parameter_set\n",
+    "        setup = IM.import_module('c302.c302_%s' % (config)).setup\n",
+    "        from c302.c302_utils import generate_conn_matrix\n",
     "\n",
-    "    nml_doc = read_neuroml2_file('images/%s'%nml_filename)\n",
-    "    nml_doc.networks[0].id = reader.replace('Reader','').replace('Spreadsheet','SS').replace('Updated','Upd')\n",
+    "        import matplotlib.pyplot as plt\n",
     "\n",
-    "    generate_conn_matrix(nml_doc, save_fig_dir='./images', figsize=(6,6))\n",
-    "        \n",
-    "print('Finished generation of images!')\n"
+    "        plt.ioff()\n",
+    "\n",
+    "        for reader_short in readers:\n",
+    "            \n",
+    "            reader_module = readers[reader_short]\n",
+    "\n",
+    "            reader = reader_module[5:]\n",
+    "\n",
+    "            print(\"\\n=== Generating using reader %s (%s)\"%(reader_module, reader_short))\n",
+    "            setup(parameter_set, \n",
+    "                  generate=True, \n",
+    "                  target_directory='images',\n",
+    "                  data_reader=reader,\n",
+    "                  verbose=False)\n",
+    "\n",
+    "            nml_filename = 'c302_%s_%s.net.nml'%(parameter_set, config)\n",
+    "\n",
+    "            nml_doc = read_neuroml2_file('images/%s'%nml_filename)\n",
+    "            nml_doc.networks[0].id = reader.replace('Reader','').replace('Spreadsheet','SS').replace('Updated','Upd')\n",
+    "            figsize=(6,6)\n",
+    "            if config=='Full' or config=='Full':\n",
+    "                figsize=(10,10)\n",
+    "            generate_conn_matrix(nml_doc, save_fig_dir='./images/%s'%config, figsize=figsize)\n",
+    "            \n",
+    "            f.write('|![---](./images/%s/%s_exc_to_neurons.png)|![---](./images/%s/%s_inh_to_neurons.png)|![---](./images/%s/%s_elec_neurons_neurons.png)|\\n'%(config, reader_short,config, reader_short,config, reader_short))\n",
+    "\n",
+    "\n",
+    "    print('Finished generation of images!')\n"
    ]
   },
   {
@@ -541,16 +853,8 @@
    "id": "d3640706-413a-4729-850f-8073402aebd6",
    "metadata": {},
    "source": [
-    "|EXC|INH|GJ|\n",
-    "|-|-|-|\n",
-    "|![exc](./images/SSData_exc_to_neurons.png)|![inh](./images/SSData_inh_to_neurons.png)|![gj](./images/SSData_elec_neurons_neurons.png)|\n",
-    "|![exc](./images/UpdSSData_exc_to_neurons.png)|![inh](./images/UpdSSData_inh_to_neurons.png)|![gj](./images/UpdSSData_elec_neurons_neurons.png)|\n",
-    "|![exc](./images/UpdSSData2_exc_to_neurons.png)|![inh](./images/UpdSSData2_inh_to_neurons.png)|![gj](./images/UpdSSData2_elec_neurons_neurons.png)|\n",
-    "|![exc](./images/OpenWorm_exc_to_neurons.png)|![inh](./images/OpenWorm_inh_to_neurons.png)|![gj](./images/OpenWorm_elec_neurons_neurons.png)|\n",
-    "|![exc](./images/White_whole_exc_to_neurons.png)|![inh](./images/White_whole_inh_to_neurons.png)|![gj](./images/White_whole_elec_neurons_neurons.png)|\n",
-    "|![exc](./images/VarshneyData_exc_to_neurons.png)|![inh](./images/VarshneyData_inh_to_neurons.png)|![gj](./images/VarshneyData_elec_neurons_neurons.png)|\n",
-    "|![exc](./images/WitvlietData2_exc_to_neurons.png)|![inh](./images/WitvlietData2_inh_to_neurons.png)|![gj](./images/WitvlietData2_elec_neurons_neurons.png)|\n",
-    "|![exc](./images/WormNeuroAtlas_exc_to_neurons.png)|![inh](./images/WormNeuroAtlas_inh_to_neurons.png)|![gj](./images/WormNeuroAtlas_elec_neurons_neurons.png)|\n",
+    "\n",
+    "## Note: views of matrices moved to Oscillator.md etc.\n",
     "\n"
    ]
   },
diff --git a/examples/test/Oscillator.md b/examples/test/Oscillator.md
new file mode 100644
index 00000000..e95f448a
--- /dev/null
+++ b/examples/test/Oscillator.md
@@ -0,0 +1,14 @@
+|EXC|INH|GJ|
+|-|-|-|
+|![---](./images/Oscillator/SSData_exc_to_neurons.png)|![---](./images/Oscillator/SSData_inh_to_neurons.png)|![---](./images/Oscillator/SSData_elec_neurons_neurons.png)|
+|![---](./images/Oscillator/UpdSSData_exc_to_neurons.png)|![---](./images/Oscillator/UpdSSData_inh_to_neurons.png)|![---](./images/Oscillator/UpdSSData_elec_neurons_neurons.png)|
+|![---](./images/Oscillator/UpdSSData2_exc_to_neurons.png)|![---](./images/Oscillator/UpdSSData2_inh_to_neurons.png)|![---](./images/Oscillator/UpdSSData2_elec_neurons_neurons.png)|
+|![---](./images/Oscillator/OpenWorm_exc_to_neurons.png)|![---](./images/Oscillator/OpenWorm_inh_to_neurons.png)|![---](./images/Oscillator/OpenWorm_elec_neurons_neurons.png)|
+|![---](./images/Oscillator/White_A_exc_to_neurons.png)|![---](./images/Oscillator/White_A_inh_to_neurons.png)|![---](./images/Oscillator/White_A_elec_neurons_neurons.png)|
+|![---](./images/Oscillator/White_L4_exc_to_neurons.png)|![---](./images/Oscillator/White_L4_inh_to_neurons.png)|![---](./images/Oscillator/White_L4_elec_neurons_neurons.png)|
+|![---](./images/Oscillator/White_whole_exc_to_neurons.png)|![---](./images/Oscillator/White_whole_inh_to_neurons.png)|![---](./images/Oscillator/White_whole_elec_neurons_neurons.png)|
+|![---](./images/Oscillator/Varshney_exc_to_neurons.png)|![---](./images/Oscillator/Varshney_inh_to_neurons.png)|![---](./images/Oscillator/Varshney_elec_neurons_neurons.png)|
+|![---](./images/Oscillator/Witvliet1_exc_to_neurons.png)|![---](./images/Oscillator/Witvliet1_inh_to_neurons.png)|![---](./images/Oscillator/Witvliet1_elec_neurons_neurons.png)|
+|![---](./images/Oscillator/Witvliet2_exc_to_neurons.png)|![---](./images/Oscillator/Witvliet2_inh_to_neurons.png)|![---](./images/Oscillator/Witvliet2_elec_neurons_neurons.png)|
+|![---](./images/Oscillator/WormNeuroAtlas_exc_to_neurons.png)|![---](./images/Oscillator/WormNeuroAtlas_inh_to_neurons.png)|![---](./images/Oscillator/WormNeuroAtlas_elec_neurons_neurons.png)|
+|![---](./images/Oscillator/Cook2019Herm_exc_to_neurons.png)|![---](./images/Oscillator/Cook2019Herm_inh_to_neurons.png)|![---](./images/Oscillator/Cook2019Herm_elec_neurons_neurons.png)|
diff --git a/examples/test/Pharyngeal.md b/examples/test/Pharyngeal.md
new file mode 100644
index 00000000..5f97afb4
--- /dev/null
+++ b/examples/test/Pharyngeal.md
@@ -0,0 +1,14 @@
+|EXC|INH|GJ|
+|-|-|-|
+|![---](./images/Pharyngeal/SSData_exc_to_neurons.png)|![---](./images/Pharyngeal/SSData_inh_to_neurons.png)|![---](./images/Pharyngeal/SSData_elec_neurons_neurons.png)|
+|![---](./images/Pharyngeal/UpdSSData_exc_to_neurons.png)|![---](./images/Pharyngeal/UpdSSData_inh_to_neurons.png)|![---](./images/Pharyngeal/UpdSSData_elec_neurons_neurons.png)|
+|![---](./images/Pharyngeal/UpdSSData2_exc_to_neurons.png)|![---](./images/Pharyngeal/UpdSSData2_inh_to_neurons.png)|![---](./images/Pharyngeal/UpdSSData2_elec_neurons_neurons.png)|
+|![---](./images/Pharyngeal/OpenWorm_exc_to_neurons.png)|![---](./images/Pharyngeal/OpenWorm_inh_to_neurons.png)|![---](./images/Pharyngeal/OpenWorm_elec_neurons_neurons.png)|
+|![---](./images/Pharyngeal/White_A_exc_to_neurons.png)|![---](./images/Pharyngeal/White_A_inh_to_neurons.png)|![---](./images/Pharyngeal/White_A_elec_neurons_neurons.png)|
+|![---](./images/Pharyngeal/White_L4_exc_to_neurons.png)|![---](./images/Pharyngeal/White_L4_inh_to_neurons.png)|![---](./images/Pharyngeal/White_L4_elec_neurons_neurons.png)|
+|![---](./images/Pharyngeal/White_whole_exc_to_neurons.png)|![---](./images/Pharyngeal/White_whole_inh_to_neurons.png)|![---](./images/Pharyngeal/White_whole_elec_neurons_neurons.png)|
+|![---](./images/Pharyngeal/Varshney_exc_to_neurons.png)|![---](./images/Pharyngeal/Varshney_inh_to_neurons.png)|![---](./images/Pharyngeal/Varshney_elec_neurons_neurons.png)|
+|![---](./images/Pharyngeal/Witvliet1_exc_to_neurons.png)|![---](./images/Pharyngeal/Witvliet1_inh_to_neurons.png)|![---](./images/Pharyngeal/Witvliet1_elec_neurons_neurons.png)|
+|![---](./images/Pharyngeal/Witvliet2_exc_to_neurons.png)|![---](./images/Pharyngeal/Witvliet2_inh_to_neurons.png)|![---](./images/Pharyngeal/Witvliet2_elec_neurons_neurons.png)|
+|![---](./images/Pharyngeal/WormNeuroAtlas_exc_to_neurons.png)|![---](./images/Pharyngeal/WormNeuroAtlas_inh_to_neurons.png)|![---](./images/Pharyngeal/WormNeuroAtlas_elec_neurons_neurons.png)|
+|![---](./images/Pharyngeal/Cook2019Herm_exc_to_neurons.png)|![---](./images/Pharyngeal/Cook2019Herm_inh_to_neurons.png)|![---](./images/Pharyngeal/Cook2019Herm_elec_neurons_neurons.png)|
diff --git a/examples/test/README.md b/examples/test/README.md
new file mode 100644
index 00000000..803fae08
--- /dev/null
+++ b/examples/test/README.md
@@ -0,0 +1,13 @@
+# Analyses of the various readers included in this package
+
+## Oscillator
+
+See [Oscillator.md](Oscillator.md)
+
+## Pharyngeal
+
+See [Pharyngeal.md](Pharyngeal.md)
+
+## Social
+
+See [Social.md](Social.md)
diff --git a/examples/test/Social.md b/examples/test/Social.md
new file mode 100644
index 00000000..6e8909b6
--- /dev/null
+++ b/examples/test/Social.md
@@ -0,0 +1,14 @@
+|EXC|INH|GJ|
+|-|-|-|
+|![---](./images/Social/SSData_exc_to_neurons.png)|![---](./images/Social/SSData_inh_to_neurons.png)|![---](./images/Social/SSData_elec_neurons_neurons.png)|
+|![---](./images/Social/UpdSSData_exc_to_neurons.png)|![---](./images/Social/UpdSSData_inh_to_neurons.png)|![---](./images/Social/UpdSSData_elec_neurons_neurons.png)|
+|![---](./images/Social/UpdSSData2_exc_to_neurons.png)|![---](./images/Social/UpdSSData2_inh_to_neurons.png)|![---](./images/Social/UpdSSData2_elec_neurons_neurons.png)|
+|![---](./images/Social/OpenWorm_exc_to_neurons.png)|![---](./images/Social/OpenWorm_inh_to_neurons.png)|![---](./images/Social/OpenWorm_elec_neurons_neurons.png)|
+|![---](./images/Social/White_A_exc_to_neurons.png)|![---](./images/Social/White_A_inh_to_neurons.png)|![---](./images/Social/White_A_elec_neurons_neurons.png)|
+|![---](./images/Social/White_L4_exc_to_neurons.png)|![---](./images/Social/White_L4_inh_to_neurons.png)|![---](./images/Social/White_L4_elec_neurons_neurons.png)|
+|![---](./images/Social/White_whole_exc_to_neurons.png)|![---](./images/Social/White_whole_inh_to_neurons.png)|![---](./images/Social/White_whole_elec_neurons_neurons.png)|
+|![---](./images/Social/Varshney_exc_to_neurons.png)|![---](./images/Social/Varshney_inh_to_neurons.png)|![---](./images/Social/Varshney_elec_neurons_neurons.png)|
+|![---](./images/Social/Witvliet1_exc_to_neurons.png)|![---](./images/Social/Witvliet1_inh_to_neurons.png)|![---](./images/Social/Witvliet1_elec_neurons_neurons.png)|
+|![---](./images/Social/Witvliet2_exc_to_neurons.png)|![---](./images/Social/Witvliet2_inh_to_neurons.png)|![---](./images/Social/Witvliet2_elec_neurons_neurons.png)|
+|![---](./images/Social/WormNeuroAtlas_exc_to_neurons.png)|![---](./images/Social/WormNeuroAtlas_inh_to_neurons.png)|![---](./images/Social/WormNeuroAtlas_elec_neurons_neurons.png)|
+|![---](./images/Social/Cook2019Herm_exc_to_neurons.png)|![---](./images/Social/Cook2019Herm_inh_to_neurons.png)|![---](./images/Social/Cook2019Herm_elec_neurons_neurons.png)|
diff --git a/examples/test/images/LEMS_c302_C1_Pharyngeal.xml b/examples/test/images/LEMS_c302_C1_Pharyngeal.xml
new file mode 100644
index 00000000..e411e344
--- /dev/null
+++ b/examples/test/images/LEMS_c302_C1_Pharyngeal.xml
@@ -0,0 +1,177 @@
+<Lems>
+    
+    <!--
+
+
+Parameters and setting used to generate this network:
+
+    Data reader:                    Cook2019HermReader
+    c302 version:                   0.8.0
+    owmeta version:                 0.12.3
+    owmeta_core version:            0.13.5
+    Cells:                          ['M1', 'M2L', 'M2R', 'M3L', 'M3R', 'M4', 'M5', 'I1L', 'I1R', 'I2L', 'I2R', 'I3', 'I4', 'I5', 'I6', 'MI', 'NSML', 'NSMR', 'MCL', 'MCR']
+    Cell stimulated:                ['M1', 'M3R', 'M4', 'M5', 'I1L', 'I4', 'I5', 'I6', 'MCL', 'MCR']
+    Connection:                     []
+    Connection numbers overridden:  None
+    Connection numbers scaled:      None
+    Connection polarities override: None
+    Muscles:                        []
+
+    Known BioParameters:
+        BioParameter: ca_boyle_erev = 40 mV (SRC: BlindGuess, certainty 0.1)
+        BioParameter: ca_conc_decay_time = 11.5943 ms (SRC: BlindGuess, certainty 0.1)
+        BioParameter: ca_conc_rho = 0.000238919 mol_per_m_per_A_per_s (SRC: BlindGuess, certainty 0.1)
+        BioParameter: cell_diameter = 5 (SRC: BlindGuess, certainty 0.1)
+        BioParameter: exc_syn_delta = 5 mV (SRC: BlindGuess, certainty 0.1)
+        BioParameter: exc_syn_erev = 0 mV (SRC: BlindGuess, certainty 0.1)
+        BioParameter: exc_syn_k = 0.025per_ms (SRC: BlindGuess, certainty 0.1)
+        BioParameter: exc_syn_vth = 0 mV (SRC: BlindGuess, certainty 0.1)
+        BioParameter: inh_syn_delta = 5 mV (SRC: BlindGuess, certainty 0.1)
+        BioParameter: inh_syn_erev = -70 mV (SRC: BlindGuess, certainty 0.1)
+        BioParameter: inh_syn_k = 0.025per_ms (SRC: BlindGuess, certainty 0.1)
+        BioParameter: inh_syn_vth = 0 mV (SRC: BlindGuess, certainty 0.1)
+        BioParameter: initial_memb_pot = -45 mV (SRC: BlindGuess, certainty 0.1)
+        BioParameter: k_fast_erev = -60 mV (SRC: BlindGuess, certainty 0.1)
+        BioParameter: k_slow_erev = -60 mV (SRC: BlindGuess, certainty 0.1)
+        BioParameter: leak_erev = -50 mV (SRC: BlindGuess, certainty 0.1)
+        BioParameter: muscle_ca_boyle_cond_density = 0.0007 S_per_cm2 (SRC: BlindGuess, certainty 0.1)
+        BioParameter: muscle_k_fast_cond_density = 0.0001 S_per_cm2 (SRC: BlindGuess, certainty 0.1)
+        BioParameter: muscle_k_slow_cond_density = 0.0006 S_per_cm2 (SRC: BlindGuess, certainty 0.1)
+        BioParameter: muscle_leak_cond_density = 5e-7 S_per_cm2 (SRC: BlindGuess, certainty 0.1)
+        BioParameter: muscle_length = 20 (SRC: BlindGuess, certainty 0.1)
+        BioParameter: muscle_spike_thresh = -20 mV (SRC: BlindGuess, certainty 0.1)
+        BioParameter: neuron_ca_boyle_cond_density = 3 mS_per_cm2 (SRC: BlindGuess, certainty 0.1)
+        BioParameter: neuron_k_fast_cond_density = 0.0711643917483308 mS_per_cm2 (SRC: BlindGuess, certainty 0.1)
+        BioParameter: neuron_k_slow_cond_density = 3 mS_per_cm2 (SRC: BlindGuess, certainty 0.1)
+        BioParameter: neuron_leak_cond_density = 0.005 mS_per_cm2 (SRC: BlindGuess, certainty 0.1)
+        BioParameter: neuron_spike_thresh = -20 mV (SRC: BlindGuess, certainty 0.1)
+        BioParameter: neuron_to_muscle_elec_syn_gbase = 0.00052 nS (SRC: BlindGuess, certainty 0.1)
+        BioParameter: neuron_to_muscle_exc_syn_conductance = 0.09 nS (SRC: BlindGuess, certainty 0.1)
+        BioParameter: neuron_to_muscle_inh_syn_conductance = 0.09 nS (SRC: BlindGuess, certainty 0.1)
+        BioParameter: neuron_to_neuron_elec_syn_gbase = 0.00052 nS (SRC: BlindGuess, certainty 0.1)
+        BioParameter: neuron_to_neuron_exc_syn_conductance = 0.09 nS (SRC: BlindGuess, certainty 0.1)
+        BioParameter: neuron_to_neuron_inh_syn_conductance = 0.09 nS (SRC: BlindGuess, certainty 0.1)
+        BioParameter: specific_capacitance = 1 uF_per_cm2 (SRC: BlindGuess, certainty 0.1)
+        BioParameter: unphysiological_offset_current = 2.2pA (SRC: Testing Pharyngeal, certainty 0)
+        BioParameter: unphysiological_offset_current_del = 50ms (SRC: Testing Pharyngeal, certainty 0)
+        BioParameter: unphysiological_offset_current_dur = 200ms (SRC: Testing Pharyngeal, certainty 0)
+
+   
+    -->
+
+    <Target component="sim_c302_C1_Pharyngeal" />
+
+    <!-- Include core NeuroML2 ComponentType definitions -->
+
+    <Include file="Cells.xml" />
+    <Include file="Networks.xml" />
+    <Include file="Simulation.xml" />
+    
+    <Include file="cell_C.xml" />
+    
+    <Include file="c302_C1_Pharyngeal.net.nml" />
+
+    <!-- End of NeuroML2 content -->
+    
+
+    <Simulation id="sim_c302_C1_Pharyngeal" length="500ms" step="0.01ms" target="c302_C1_Pharyngeal">
+
+        <Display id="neurons" title="c302_C1_Pharyngeal: Membrane potential of a number of neurons" timeScale="1ms" xmin="-50.0" xmax="550.0" ymin="-60" ymax="25">
+            
+            <Line id="I1L" quantity="I1L/0/GenericNeuronCell/v" scale="1mV" color="#e13b00" timeScale="1ms" />
+            <Line id="I1R" quantity="I1R/0/GenericNeuronCell/v" scale="1mV" color="#32b579" timeScale="1ms" />
+            <Line id="I2L" quantity="I2L/0/GenericNeuronCell/v" scale="1mV" color="#b1f7ed" timeScale="1ms" />
+            <Line id="I2R" quantity="I2R/0/GenericNeuronCell/v" scale="1mV" color="#3a00f9" timeScale="1ms" />
+            <Line id="I3" quantity="I3/0/GenericNeuronCell/v" scale="1mV" color="#232d17" timeScale="1ms" />
+            <Line id="I4" quantity="I4/0/GenericNeuronCell/v" scale="1mV" color="#f6b588" timeScale="1ms" />
+            <Line id="I5" quantity="I5/0/GenericNeuronCell/v" scale="1mV" color="#002400" timeScale="1ms" />
+            <Line id="I6" quantity="I6/0/GenericNeuronCell/v" scale="1mV" color="#c1551b" timeScale="1ms" />
+            <Line id="M1" quantity="M1/0/GenericNeuronCell/v" scale="1mV" color="#266e49" timeScale="1ms" />
+            <Line id="M2L" quantity="M2L/0/GenericNeuronCell/v" scale="1mV" color="#489ce8" timeScale="1ms" />
+            <Line id="M2R" quantity="M2R/0/GenericNeuronCell/v" scale="1mV" color="#145a8b" timeScale="1ms" />
+            <Line id="M3L" quantity="M3L/0/GenericNeuronCell/v" scale="1mV" color="#ed15c5" timeScale="1ms" />
+            <Line id="M3R" quantity="M3R/0/GenericNeuronCell/v" scale="1mV" color="#eff317" timeScale="1ms" />
+            <Line id="M4" quantity="M4/0/GenericNeuronCell/v" scale="1mV" color="#e0978c" timeScale="1ms" />
+            <Line id="M5" quantity="M5/0/GenericNeuronCell/v" scale="1mV" color="#df3d34" timeScale="1ms" />
+            <Line id="MCL" quantity="MCL/0/GenericNeuronCell/v" scale="1mV" color="#62b037" timeScale="1ms" />
+            <Line id="MCR" quantity="MCR/0/GenericNeuronCell/v" scale="1mV" color="#a5e424" timeScale="1ms" />
+            <Line id="MI" quantity="MI/0/GenericNeuronCell/v" scale="1mV" color="#189213" timeScale="1ms" />
+            <Line id="NSML" quantity="NSML/0/GenericNeuronCell/v" scale="1mV" color="#9ceb21" timeScale="1ms" />
+            <Line id="NSMR" quantity="NSMR/0/GenericNeuronCell/v" scale="1mV" color="#6733cb" timeScale="1ms" />
+            
+        </Display>
+      
+        <Display id="activity_neurons" title="c302_C1_Pharyngeal: Activity of a number of neurons" timeScale="1ms" xmin="-50.0" xmax="550.0" ymin="-0.1" ymax="1.1">
+            
+            <Line id="I1L" quantity="I1L/0/GenericNeuronCell/caConc" scale="1" color="#2e112a" timeScale="1ms" />
+            <Line id="I1R" quantity="I1R/0/GenericNeuronCell/caConc" scale="1" color="#000000" timeScale="1ms" />
+            <Line id="I2L" quantity="I2L/0/GenericNeuronCell/caConc" scale="1" color="#4c2e5d" timeScale="1ms" />
+            <Line id="I2R" quantity="I2R/0/GenericNeuronCell/caConc" scale="1" color="#7f21ee" timeScale="1ms" />
+            <Line id="I3" quantity="I3/0/GenericNeuronCell/caConc" scale="1" color="#8a209a" timeScale="1ms" />
+            <Line id="I4" quantity="I4/0/GenericNeuronCell/caConc" scale="1" color="#7f66e8" timeScale="1ms" />
+            <Line id="I5" quantity="I5/0/GenericNeuronCell/caConc" scale="1" color="#aa49f2" timeScale="1ms" />
+            <Line id="I6" quantity="I6/0/GenericNeuronCell/caConc" scale="1" color="#27fe53" timeScale="1ms" />
+            <Line id="M1" quantity="M1/0/GenericNeuronCell/caConc" scale="1" color="#00b138" timeScale="1ms" />
+            <Line id="M2L" quantity="M2L/0/GenericNeuronCell/caConc" scale="1" color="#14d58d" timeScale="1ms" />
+            <Line id="M2R" quantity="M2R/0/GenericNeuronCell/caConc" scale="1" color="#4f994f" timeScale="1ms" />
+            <Line id="M3L" quantity="M3L/0/GenericNeuronCell/caConc" scale="1" color="#b2fdae" timeScale="1ms" />
+            <Line id="M3R" quantity="M3R/0/GenericNeuronCell/caConc" scale="1" color="#f157e1" timeScale="1ms" />
+            <Line id="M4" quantity="M4/0/GenericNeuronCell/caConc" scale="1" color="#3f5fd5" timeScale="1ms" />
+            <Line id="M5" quantity="M5/0/GenericNeuronCell/caConc" scale="1" color="#f8c082" timeScale="1ms" />
+            <Line id="MCL" quantity="MCL/0/GenericNeuronCell/caConc" scale="1" color="#50894f" timeScale="1ms" />
+            <Line id="MCR" quantity="MCR/0/GenericNeuronCell/caConc" scale="1" color="#28ca6d" timeScale="1ms" />
+            <Line id="MI" quantity="MI/0/GenericNeuronCell/caConc" scale="1" color="#702ca2" timeScale="1ms" />
+            <Line id="NSML" quantity="NSML/0/GenericNeuronCell/caConc" scale="1" color="#8325da" timeScale="1ms" />
+            <Line id="NSMR" quantity="NSMR/0/GenericNeuronCell/caConc" scale="1" color="#63eb00" timeScale="1ms" />
+
+        </Display>
+
+        <OutputFile id="neurons_v" fileName="c302_C1_Pharyngeal.dat">
+            <OutputColumn id="I1L_v" quantity="I1L/0/GenericNeuronCell/v"/>
+            <OutputColumn id="I1R_v" quantity="I1R/0/GenericNeuronCell/v"/>
+            <OutputColumn id="I2L_v" quantity="I2L/0/GenericNeuronCell/v"/>
+            <OutputColumn id="I2R_v" quantity="I2R/0/GenericNeuronCell/v"/>
+            <OutputColumn id="I3_v" quantity="I3/0/GenericNeuronCell/v"/>
+            <OutputColumn id="I4_v" quantity="I4/0/GenericNeuronCell/v"/>
+            <OutputColumn id="I5_v" quantity="I5/0/GenericNeuronCell/v"/>
+            <OutputColumn id="I6_v" quantity="I6/0/GenericNeuronCell/v"/>
+            <OutputColumn id="M1_v" quantity="M1/0/GenericNeuronCell/v"/>
+            <OutputColumn id="M2L_v" quantity="M2L/0/GenericNeuronCell/v"/>
+            <OutputColumn id="M2R_v" quantity="M2R/0/GenericNeuronCell/v"/>
+            <OutputColumn id="M3L_v" quantity="M3L/0/GenericNeuronCell/v"/>
+            <OutputColumn id="M3R_v" quantity="M3R/0/GenericNeuronCell/v"/>
+            <OutputColumn id="M4_v" quantity="M4/0/GenericNeuronCell/v"/>
+            <OutputColumn id="M5_v" quantity="M5/0/GenericNeuronCell/v"/>
+            <OutputColumn id="MCL_v" quantity="MCL/0/GenericNeuronCell/v"/>
+            <OutputColumn id="MCR_v" quantity="MCR/0/GenericNeuronCell/v"/>
+            <OutputColumn id="MI_v" quantity="MI/0/GenericNeuronCell/v"/>
+            <OutputColumn id="NSML_v" quantity="NSML/0/GenericNeuronCell/v"/>
+            <OutputColumn id="NSMR_v" quantity="NSMR/0/GenericNeuronCell/v"/>
+        </OutputFile>
+        
+        <OutputFile id="neurons_activity" fileName="c302_C1_Pharyngeal.activity.dat">
+            <OutputColumn id="I1L_v" quantity="I1L/0/GenericNeuronCell/caConc"/>
+            <OutputColumn id="I1R_v" quantity="I1R/0/GenericNeuronCell/caConc"/>
+            <OutputColumn id="I2L_v" quantity="I2L/0/GenericNeuronCell/caConc"/>
+            <OutputColumn id="I2R_v" quantity="I2R/0/GenericNeuronCell/caConc"/>
+            <OutputColumn id="I3_v" quantity="I3/0/GenericNeuronCell/caConc"/>
+            <OutputColumn id="I4_v" quantity="I4/0/GenericNeuronCell/caConc"/>
+            <OutputColumn id="I5_v" quantity="I5/0/GenericNeuronCell/caConc"/>
+            <OutputColumn id="I6_v" quantity="I6/0/GenericNeuronCell/caConc"/>
+            <OutputColumn id="M1_v" quantity="M1/0/GenericNeuronCell/caConc"/>
+            <OutputColumn id="M2L_v" quantity="M2L/0/GenericNeuronCell/caConc"/>
+            <OutputColumn id="M2R_v" quantity="M2R/0/GenericNeuronCell/caConc"/>
+            <OutputColumn id="M3L_v" quantity="M3L/0/GenericNeuronCell/caConc"/>
+            <OutputColumn id="M3R_v" quantity="M3R/0/GenericNeuronCell/caConc"/>
+            <OutputColumn id="M4_v" quantity="M4/0/GenericNeuronCell/caConc"/>
+            <OutputColumn id="M5_v" quantity="M5/0/GenericNeuronCell/caConc"/>
+            <OutputColumn id="MCL_v" quantity="MCL/0/GenericNeuronCell/caConc"/>
+            <OutputColumn id="MCR_v" quantity="MCR/0/GenericNeuronCell/caConc"/>
+            <OutputColumn id="MI_v" quantity="MI/0/GenericNeuronCell/caConc"/>
+            <OutputColumn id="NSML_v" quantity="NSML/0/GenericNeuronCell/caConc"/>
+            <OutputColumn id="NSMR_v" quantity="NSMR/0/GenericNeuronCell/caConc"/>
+        </OutputFile>
+    </Simulation>
+
+
+</Lems>
diff --git a/examples/test/images/Oscillator/Cook2019Herm_elec_neurons_neurons.png b/examples/test/images/Oscillator/Cook2019Herm_elec_neurons_neurons.png
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similarity index 100%
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rename to examples/test/images/Oscillator/OpenWorm_elec_neurons_neurons.png
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rename from examples/test/images/SSData_elec_neurons_neurons.png
rename to examples/test/images/Oscillator/SSData_elec_neurons_neurons.png
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rename from examples/test/images/UpdSSData2_elec_neurons_neurons.png
rename to examples/test/images/Oscillator/UpdSSData2_elec_neurons_neurons.png
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rename from examples/test/images/UpdSSData2_exc_to_neurons.png
rename to examples/test/images/Oscillator/UpdSSData2_exc_to_neurons.png
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rename to examples/test/images/Oscillator/UpdSSData_elec_neurons_neurons.png
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