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neurodata · Jan 3, 2024 · 41d6284 · 41d6284
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commit 41d6284
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Showing 3 changed files with 155 additions and 19 deletions.
diff --git a/experiments/BrainLine/data/soma_data.json b/experiments/BrainLine/data/soma_data.json
@@ -340,6 +340,16 @@
             },
             "subtype": "tph2 gad2",
             "somas_atlas_path": "/Users/thomasathey/Documents/mimlab/mouselight/ailey/detection_soma/wholebrain_results/atlas_somas_MS21/"
+        },
+        "1252B": {
+            "base_local": "precomputed://file:///mnt/data/Neuroglancer_Data/2023_12_20/1252B/",
+            "base_s3": "precomputed://s3://smartspim-precomputed-volumes/2023_12_20/1252B/",
+            "val_info": {
+                "url": "https://viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=zgiW1wL8q-E4mg",
+                "somas_layer": "soma_val",
+                "nonsomas_layer": "nonsoma_val"
+            },
+            "subtype": "tph2 vglut3"
         }
     },
     "brain2centers": {

diff --git a/experiments/BrainLine/scripts/soma_detect_image.py b/experiments/BrainLine/scripts/soma_detect_image.py
@@ -9,12 +9,12 @@
 # -dir_base
 # data_dir and results_dir ARE CLEAR
 # threshold IS CORRECT
-brain = "MS50_v2"
+brain = "1252B"
 antibody_layer = "Ch_647"
 background_layer = "Ch_561"
 endogenous_layer = "Ch_488"
 
-threshold = 0.72  # threshold to use for ilastik
+threshold = 0.7  # threshold to use for ilastik
 brainline_exp_dir = Path(os.getcwd()) / Path(__file__).parents[1]
 data_dir = (
     brainline_exp_dir / "data" / "brainr_temp"
@@ -39,7 +39,7 @@
     -1,
 ]  # max coords or -1 if you want to process everything along that dimension
 max_coords = [
-    5957,
+    6097,
     11000,
     -1,
 ]  # max coords or -1 if you want to process everything along that dimension

diff --git a/experiments/BrainLine/soma_analysis.ipynb b/experiments/BrainLine/soma_analysis.ipynb