Merge pull request #411 from Hjorthmedh/dev

New config formats
Hjorthmedh · Mar 1, 2024 · 7a950ed · 7a950ed
2 parents 3ab4136 + 1525b9c
commit 7a950ed
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diff --git a/examples/example_config/network.json b/examples/example_config/network.json
@@ -0,0 +1,12 @@
+{
+    "network_path": "my_network",
+    "snudda_data": "/home/hjorth/HBP/BasalGangliaData/data",
+
+    "random_seed": {
+	"master_seed": 1234	
+    },
+
+    "regions": {
+	"Striatum" : "striatum.json"
+    }	
+}
diff --git a/examples/example_config/neurons/chin.json b/examples/example_config/neurons/chin.json
@@ -0,0 +1,18 @@
+{
+    "ChIN": {
+	"neuron_path": {
+	    "ChIN_0": "$SNUDDA_DATA/neurons/striatum/chin/str-chin-e170614_cell6-m17JUL301751_170614_no6_MD_cell_1_x63-v20190710"
+	},
+
+	"neuron_type": "neuron",	    
+	"rotation_mode": "random",
+	"volume_id": "Striatum",
+	"stay_inside_mesh": false,
+	"fraction": 0.011,
+	"axon_density": [
+            "r",
+            "5000*1e12/3*exp(-r/120e-6)",
+            0.00035
+	]
+    }	
+}
diff --git a/examples/example_config/neurons/dspn.json b/examples/example_config/neurons/dspn.json
@@ -0,0 +1,17 @@
+{
+    "dSPN": {
+	"neuron_path": {
+	    "dSPN_0": "$SNUDDA_DATA/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026",
+	    "dSPN_1": "$SNUDDA_DATA/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026",
+	    "dSPN_2": "$SNUDDA_DATA/neurons/striatum/dspn/str-dspn-e150917_c6_D1-m21-6-DE-v20211028",
+	    "dSPN_3": "$SNUDDA_DATA/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026"
+	},
+
+	"neuron_type": "neuron",
+	"rotation_mode": "random",
+	"volume_id": "Striatum",
+	"stay_inside_mesh": false,
+	"fraction": 0.475
+    }
+
+}
diff --git a/examples/example_config/neurons/fs.json b/examples/example_config/neurons/fs.json
@@ -0,0 +1,16 @@
+{
+    "FS": {
+	"neuron_path": {
+	    "FS_0": "$SNUDDA_DATA/neurons/striatum/fs/str-fs-e160628_FS2-mMTC180800A-IDB-v20210210",
+	    "FS_1": "$SNUDDA_DATA/neurons/striatum/fs/str-fs-e161024_FS16-mDR-rat-Mar-13-08-1-536-R-v20210210",
+	    "FS_2": "$SNUDDA_DATA/neurons/striatum/fs/str-fs-e161205_FS1-mBE104E-v20210209",
+	    "FS_3": "$SNUDDA_DATA/neurons/striatum/fs/str-fs-e161205_FS1-mMTC180800A-IDB-v20210210"
+	},
+
+        "neuron_type": "neuron",
+        "rotation_mode": "random",
+        "volume_id": "Striatum",
+	"stay_inside_mesh": false,
+        "fraction": 0.013
+    }
+}
diff --git a/examples/example_config/neurons/ispn.json b/examples/example_config/neurons/ispn.json
@@ -0,0 +1,16 @@
+{
+    "iSPN": {
+	"neuron_path": {
+	    "iSPN_0": "$SNUDDA_DATA/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026",
+	    "iSPN_1": "$SNUDDA_DATA/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026",
+	    "iSPN_2": "$SNUDDA_DATA/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026",
+	    "iSPN_3": "$SNUDDA_DATA/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026"
+	},
+
+        "neuron_type": "neuron",
+        "rotation_mode": "random",
+        "volume_id": "Striatum",
+	"stay_inside_mesh": false,
+        "fraction": 0.475
+    }
+}
diff --git a/examples/example_config/neurons/lts.json b/examples/example_config/neurons/lts.json
@@ -0,0 +1,27 @@
+{
+    "LTS": {
+	"neuron_path" : {
+	    "LTS_0" : "$SNUDDA_DATA/neurons/striatum/lts/LTS_180118_morp_9862_updated_20210301",
+	    "LTS_1" : "$SNUDDA_DATA/neurons/striatum/lts/LTS_180118_morp_9862_updated_April2022"	    
+	},
+
+        "neuron_type": "neuron",
+        "rotation_mode": "random",
+        "volume_id": "Striatum",
+	"stay_inside_mesh": false,
+        "fraction": 0.007,
+        "axon_density": [
+            "xyz",
+            "12*3000*1e12*( 0.25*exp(-(((x-200e-6)/100e-6)**2 + ((y-0)/50e-6)**2 + ((z-0)/30e-6)**2)) + 1*exp(-(((x-300e-6)/300e-6)**2 + ((y-0)/15e-6)**2 + ((z-0)/10e-6)**2)) + 1*exp(-(((x-700e-6)/100e-6)**2 + ((y-0)/15e-6)**2 + ((z-0)/15e-6)**2)) )",
+            [
+                -0.0002,
+                0.0009,
+                -0.0001,
+                0.0001,
+                -3e-05,
+                3e-05
+            ]
+        ]
+    }
+}
+
diff --git a/examples/example_config/pop1.json b/examples/example_config/pop1.json
@@ -0,0 +1,16 @@
+{
+    "populations": {
+	"method": "radial_density",
+        "centres": [[ 0.00475, 0.004, 0.00775 ],
+		    [ 0.00475, 0.004, 0.00775 ]],
+        "probability_functions": [
+            "(d < 300e-6) * 1",
+            "(d < 300e-6) * 1"
+        ],
+        "unit_id": [ 1, 2 ],
+        "neuron_types": [["dSPN", "iSPN"],
+			 ["dSPN", "iSPN"]],
+        "num_neurons": [ 4000, 4000 ]
+
+    }   
+}
diff --git a/examples/example_config/striatum.json b/examples/example_config/striatum.json
@@ -0,0 +1,29 @@
+{
+    "Striatum": {
+	"num_neurons": 1000,
+	"volume": {
+	    "mesh_file": "$SNUDDA_DATA/meshes/Striatum-dorsal-left-hemisphere.obj",
+	    "d_min": 1.5e-5,
+	    "num_putative_points": 100000,
+	    "random_seed": 123456,
+	    "!density": {
+		"my_neuron": {
+		    "density_function": "abs(x)"
+		}
+	    },
+	    "!neuron_orientation": {
+		"my_neuron": {
+		    "rotation_mode": "vector_field",
+		    "rotation_field_file": "my_rotation_file.json"
+		}
+	    }
+	},
+	"neurons": ["neurons/dspn.json",
+		    "neurons/ispn.json",
+		    "neurons/fs.json",
+		    "neurons/chin.json",
+		    "neurons/lts.json"],
+	"connectivity": ["$SNUDDA_DATA/connectivity/striatum/striatum-connectivity.json"],
+	"populations": "pop1.json"
+    }
+}