Merge pull request #19 from pgleeson/main

Add initial Bentley monaminergic/peptidergic info

cect/Cells.py

@@ -27,6 +27,12 @@
     "Serotonin_Glutamate",
 ]
 
+EXTRASYNAPTIC_SYN_TYPE = "Extrasynaptic"
+MONOAMINERGIC_SYN_CLASS = "Monoaminergic"
+PEPTIDERGIC_SYN_CLASS = "Peptidergic"
+
+ALL_KNOWN_EXTRASYNAPTIC_CLASSES = [MONOAMINERGIC_SYN_CLASS, PEPTIDERGIC_SYN_CLASS]
+
 cell_notes = {}
 
 connectomes = None

cect/Comparison.py

@@ -33,6 +33,8 @@
     "SSData": "SSDR_data",
     "UpdSSData": "UpdSSData_data",
     "UpdSSData2": "UpdSSData2_data",
+    "Bentley2016_MA": "Bentley2016_MA_data",
+    "Bentley2016_PEP": "Bentley2016_PEP_data",
 }
 
 all_data[""] = [
@@ -129,8 +131,10 @@ def generate_comparison_page(quick: bool, color_table=True):
         "Cook2020": ["cect.Cook2020DataReader", "Cook_2020"],
         "Witvliet1": ["cect.WitvlietDataReader1", "Witvliet_2021"],
     }
+    # readers = {}
 
-    readers["Randi2023"] = ["cect.WormNeuroAtlasFuncReader", "Randi_2023"]
+    readers["Bentley2016_MA"] = ["cect.WormNeuroAtlasMAReader", "Bentley_2016"]
+    readers["Bentley2016_PEP"] = ["cect.WormNeuroAtlasPepReader", "Bentley_2016"]
 
     if not quick:
         readers["Witvliet2"] = ["cect.WitvlietDataReader2", "Witvliet_2021"]
@@ -142,9 +146,10 @@ def generate_comparison_page(quick: bool, color_table=True):
         readers["Witvliet8"] = ["cect.WitvlietDataReader8", "Witvliet_2021"]
         readers["White_A"] = ["cect.White_A", "White_1986"]
         readers["White_L4"] = ["cect.White_L4", "White_1986"]
-        readers["WormNeuroAtlas"] = ["cect.WormNeuroAtlasReader", "Randi_2023"]
         readers["Cook2019Herm"] = ["cect.Cook2019HermReader", "Cook_2019"]
         readers["Cook2019Male"] = ["cect.Cook2019MaleReader", "Cook_2019"]
+        readers["WormNeuroAtlas"] = ["cect.WormNeuroAtlasReader", "Randi_2023"]
+        readers["Randi2023"] = ["cect.WormNeuroAtlasFuncReader", "Randi_2023"]
 
     main_mk = "# Comparison between data readers\n"
     table = ""

cect/ConnectomeView.py

@@ -19,6 +19,7 @@
 from cect.Cells import PHARYNGEAL_MOTORNEURONS
 
 from cect.Cells import ALL_KNOWN_CHEMICAL_NEUROTRANSMITTERS
+from cect.Cells import ALL_KNOWN_EXTRASYNAPTIC_CLASSES
 
 from cect.Cells import get_standard_color
 
@@ -93,6 +94,7 @@ def get_index_of_cell(self, cell):
     "Chemical Exc": ["Generic_CS"] + putative_exc_syn_class,
     "Chemical Inh": ["GABA"],
     "Electrical": ["Generic_GJ"],
+    "Extrasynaptic": ALL_KNOWN_EXTRASYNAPTIC_CLASSES,
 }
 
 EXC_INH_GJ_FUNC_SYN_CLASSES = copy.deepcopy(EXC_INH_GJ_SYN_CLASSES)
@@ -103,6 +105,7 @@ def get_index_of_cell(self, cell):
     "Chemical": EXC_INH_GJ_SYN_CLASSES["Chemical Exc"]
     + EXC_INH_GJ_SYN_CLASSES["Chemical Inh"],
     "Electrical": ["Generic_GJ"],
+    "Extrasynaptic": EXC_INH_GJ_SYN_CLASSES["Extrasynaptic"],
 }
 
 CHEM_GJ_FUNC_SYN_CLASSES = copy.deepcopy(CHEM_GJ_SYN_CLASSES)

cect/WormNeuroAtlasExtSynReader.py

@@ -0,0 +1,129 @@
+import logging
+
+from cect.ConnectomeReader import ConnectionInfo
+from cect.ConnectomeDataset import ConnectomeDataset
+from cect.Cells import EXTRASYNAPTIC_SYN_TYPE
+from cect.Cells import MONOAMINERGIC_SYN_CLASS
+from cect.Cells import PEPTIDERGIC_SYN_CLASS
+
+from cect import print_
+
+import wormneuroatlas as wa
+import sys
+
+from cect.WormNeuroAtlasReader import get_all_cells
+
+
+############################################################
+
+#   A script to read the values in WormNeuroAtlas
+
+############################################################
+
+LOGGER = logging.getLogger(__name__)
+
+READER_DESCRIPTION = """Data extracted from the **WormNeuroAtlas package** for extrasynaptic connectivity"""
+
+
+class WormNeuroAtlasExtSynReader(ConnectomeDataset):
+    def __init__(self, synclass):
+        ConnectomeDataset.__init__(self)
+
+        self.synclass = synclass
+
+        print_(
+            "Initialising WormNeuroAtlasExtSynReader for syn class %s" % self.synclass
+        )
+
+        self.atlas = wa.NeuroAtlas()
+
+        self.all_cells = get_all_cells(self.atlas)
+
+        cells, neuron_conns = self.read_data()
+
+        for conn in neuron_conns:
+            self.add_connection_info(conn)
+
+    def read_data(self):
+        conns = []
+
+        if self.synclass == MONOAMINERGIC_SYN_CLASS:
+            connectome = self.atlas.get_monoaminergic_connectome()
+            syntype = EXTRASYNAPTIC_SYN_TYPE
+
+        if self.synclass == PEPTIDERGIC_SYN_CLASS:
+            connectome = self.atlas.get_peptidergic_connectome()
+            syntype = EXTRASYNAPTIC_SYN_TYPE
+
+        connected_cells = []
+
+        for pre in self.all_cells:
+            apre = self.atlas.ids_to_ai([pre])
+            for post in self.all_cells:
+                apost = self.atlas.ids_to_ai([post])
+
+                connection = False
+
+                weight = connectome[apost, apre][0]
+
+                if weight != 0:
+                    print(
+                        "%s conn (%s (%i) -> %s (%i):\t%s "
+                        % (self.synclass, pre, apre, post, apost, weight)
+                    )
+                    conns.append(
+                        ConnectionInfo(pre, post, weight, syntype, self.synclass)
+                    )
+                    connection = True
+
+                if connection:
+                    if pre not in connected_cells:
+                        connected_cells.append(pre)
+                    if post not in connected_cells:
+                        connected_cells.append(post)
+
+        return connected_cells, conns
+
+    def read_muscle_data(self):
+        neurons = []
+        muscles = []
+        conns = []
+        return neurons, muscles, conns
+
+
+if __name__ == "__main__":
+    syn_class_to_test = PEPTIDERGIC_SYN_CLASS
+
+    my_instance = WormNeuroAtlasExtSynReader(syn_class_to_test)
+    cells, neuron_conns = my_instance.read_data()
+    print("Loaded %s connections" % len(neuron_conns))
+
+    # from cect.ConnectomeReader import analyse_connections
+    # analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_conns)
+
+    to_test = ["RIMR"]
+
+    for cell in to_test:
+        my_instance.atlas.all_about(cell)
+
+        print(
+            "MA conns from %s: %s"
+            % (
+                cell,
+                my_instance.get_connections_from(
+                    cell, syn_class_to_test, ordered_by_weight=True
+                ),
+            )
+        )
+        print(
+            "MA conns to %s: %s"
+            % (
+                cell,
+                my_instance.get_connections_to(
+                    cell, syn_class_to_test, ordered_by_weight=True
+                ),
+            )
+        )
+
+    if "-nogui" not in sys.argv:
+        my_instance.connection_number_plot(syn_class_to_test)

cect/WormNeuroAtlasMAReader.py

@@ -0,0 +1,60 @@
+############################################################
+
+#   A script to read the values in WormNeuroAtlas
+
+############################################################
+
+from cect.WormNeuroAtlasExtSynReader import WormNeuroAtlasExtSynReader
+from cect.Cells import MONOAMINERGIC_SYN_CLASS
+
+import logging
+import sys
+
+
+LOGGER = logging.getLogger(__name__)
+
+READER_DESCRIPTION = """Data extracted from the **WormNeuroAtlas package** for monoaminergic connectivity"""
+
+
+def get_instance():
+    return WormNeuroAtlasExtSynReader(MONOAMINERGIC_SYN_CLASS)
+
+
+my_instance = get_instance()
+
+read_data = my_instance.read_data
+read_muscle_data = my_instance.read_muscle_data
+
+if __name__ == "__main__":
+    cells, neuron_conns = my_instance.read_data()
+    print("Loaded %s connections" % len(neuron_conns))
+
+    # from cect.ConnectomeReader import analyse_connections
+    # analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_conns)
+
+    to_test = ["ADAL", "MCL", "M5"]
+
+    for cell in to_test:
+        my_instance.atlas.all_about(cell)
+
+        print(
+            "MA conns from %s: %s"
+            % (
+                cell,
+                my_instance.get_connections_from(
+                    cell, MONOAMINERGIC_SYN_CLASS, ordered_by_weight=True
+                ),
+            )
+        )
+        print(
+            "MA conns to %s: %s"
+            % (
+                cell,
+                my_instance.get_connections_to(
+                    cell, MONOAMINERGIC_SYN_CLASS, ordered_by_weight=True
+                ),
+            )
+        )
+
+    if "-nogui" not in sys.argv:
+        my_instance.connection_number_plot(MONOAMINERGIC_SYN_CLASS)

cect/WormNeuroAtlasPepReader.py

@@ -0,0 +1,62 @@
+############################################################
+
+#   A script to read the values in WormNeuroAtlas
+
+############################################################
+
+from cect.WormNeuroAtlasExtSynReader import WormNeuroAtlasExtSynReader
+from cect.Cells import PEPTIDERGIC_SYN_CLASS
+
+import logging
+import sys
+
+
+LOGGER = logging.getLogger(__name__)
+
+READER_DESCRIPTION = """Data extracted from the **WormNeuroAtlas package** for peptidergic connectivity"""
+
+
+def get_instance():
+    return WormNeuroAtlasExtSynReader(PEPTIDERGIC_SYN_CLASS)
+
+
+my_instance = get_instance()
+
+read_data = my_instance.read_data
+read_muscle_data = my_instance.read_muscle_data
+
+if __name__ == "__main__":
+    syn_class_to_test = PEPTIDERGIC_SYN_CLASS
+
+    cells, neuron_conns = my_instance.read_data()
+    print("Loaded %s connections" % len(neuron_conns))
+
+    # from cect.ConnectomeReader import analyse_connections
+    # analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_conns)
+
+    to_test = ["ADAL", "MCL", "M5"]
+
+    for cell in to_test:
+        my_instance.atlas.all_about(cell)
+
+        print(
+            "MA conns from %s: %s"
+            % (
+                cell,
+                my_instance.get_connections_from(
+                    cell, syn_class_to_test, ordered_by_weight=True
+                ),
+            )
+        )
+        print(
+            "MA conns to %s: %s"
+            % (
+                cell,
+                my_instance.get_connections_to(
+                    cell, syn_class_to_test, ordered_by_weight=True
+                ),
+            )
+        )
+
+    if "-nogui" not in sys.argv:
+        my_instance.connection_number_plot(syn_class_to_test)