new soma

neurodata · Jan 10, 2024 · 83a89be · 83a89be
1 parent 35a1b2b
commit 83a89be
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Showing 3 changed files with 518 additions and 47 deletions.
diff --git a/experiments/BrainLine/axon_analysis.ipynb b/experiments/BrainLine/axon_analysis.ipynb
diff --git a/experiments/BrainLine/data/soma_data.json b/experiments/BrainLine/data/soma_data.json
@@ -233,7 +233,6 @@
         },
         "MS25": {
             "base_s3": "precomputed://file:///mnt/data/Neuroglancer_Data/2023_04_14/MS25/",
-            "base_s3": "precomputed://s3://smartspim-precomputed-volumes/2023_04_14/MS25/",
             "val_info": {
                 "url": "https://viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=s76nWlFZjjg-lQ",
                 "somas_layer": "soma_val",
@@ -283,6 +282,16 @@
                 "somas_layer": "soma_val",
                 "nonsomas_layer": "nonsoma_val"
             },
+            "starter_train_info": {
+                "url": "https://viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=uiGhai7eTPU8xg",
+                "somas_layer": "start_train",
+                "nonsomas_layer": "nonstart_train"
+            },
+            "starter_val_info": {
+                "url": "https://viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=Vm-cDYnBgMZCEg",
+                "somas_layer": "start_val",
+                "nonsomas_layer": "nonstart_val"
+            },
             "subtype": "tph2 gad2",
             "somas_atlas_path": "/Users/thomasathey/Documents/mimlab/mouselight/ailey/detection_soma/wholebrain_results/atlas_somas_MS23/",
             "somas_atlas_url": "https://ara.viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=haZlIiduEDJlOA"
@@ -294,6 +303,11 @@
                 "somas_layer": "soma_val",
                 "nonsomas_layer": "nonsoma_val"
             },
+            "starter_val_info": {
+                "url": "https://viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=cewxv5X_nL9P2w",
+                "somas_layer": "start_val",
+                "nonsomas_layer": "nonstart_val"
+            },
             "subtype": "tph2 gad2",
             "somas_atlas_url": "https://ara.viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=GARK_nAwpm9gAA"
         },
@@ -348,6 +362,17 @@
                 "somas_layer": "soma_val",
                 "nonsomas_layer": "nonsoma_val"
             },
+            "subtype": "tph2 vglut3",
+            "somas_atlas_path": "/Users/thomasathey/Documents/mimlab/mouselight/ailey/detection_soma/wholebrain_results/atlas_somas_1252B/"
+        },
+        "8030R": {
+            "base_local": "precomputed://file:///mnt/data/Neuroglancer_Data/2024_01_02/8030R/",
+            "base_s3": "precomputed://s3://smartspim-precomputed-volumes/2024_01_02/8030R/",
+            "val_info": {
+                "url": "https://viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=2IOg-6dGysMKyA",
+                "somas_layer": "soma_val",
+                "nonsomas_layer": "nonsoma_val"
+            },
             "subtype": "tph2 vglut3"
         }
     },