more samples

neurodata · Jul 22, 2024 · ff30ec2 · ff30ec2
1 parent b30ef10
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diff --git a/brainlit/BrainLine/apply_ilastik.py b/brainlit/BrainLine/apply_ilastik.py
@@ -551,7 +551,7 @@ def apply_ilastik_parallel(
         """
         results_dir = self.results_dir
         volume_base_dir_read = self.brain2paths[brain_id]["base_local"]
-        volume_base_dir_write = self.brain2paths[brain_id]["base_s3"]
+        volume_base_dir_write = self.brain2paths[brain_id]["base_local"]
         sample_path = volume_base_dir_read + layer_names[1]
         vol = CloudVolume(sample_path, parallel=True, mip=0, fill_missing=True)
         shape = vol.shape

diff --git a/experiments/BrainLine/axon_analysis.ipynb b/experiments/BrainLine/axon_analysis.ipynb
diff --git a/experiments/BrainLine/data/axon_data.json b/experiments/BrainLine/data/axon_data.json
@@ -245,6 +245,7 @@
         },
         "MS14": {
             "base_s3": "precomputed://s3://smartspim-precomputed-volumes/2023_04_11/MS14/",
+            "base_local": "precomputed://file:///mnt/data/Neuroglancer_Data/2023_04_11/MS14/",
             "val_info": {
                 "url": "https://viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=Nlv--2uxdrewZw",
                 "layer": "val"

diff --git a/experiments/BrainLine/data/models/axon/axon_segmentation.ilp b/experiments/BrainLine/data/models/axon/axon_segmentation.ilp
diff --git a/experiments/BrainLine/data/models/soma/matt_soma_rabies_pix_3ch.ilp b/experiments/BrainLine/data/models/soma/matt_soma_rabies_pix_3ch.ilp
diff --git a/experiments/BrainLine/data/soma_data.json b/experiments/BrainLine/data/soma_data.json
diff --git a/experiments/BrainLine/scripts/axon_segment_image.py b/experiments/BrainLine/scripts/axon_segment_image.py
@@ -33,15 +33,14 @@
 data_file = brainline_exp_dir / "data" / "axon_data.json"
 
 # Ilastik will run in "headless mode", and the following paths are needed to do so:
-ilastik_path = "/Applications/ilastik-1.4.0b21-OSX.app/Contents/ilastik-release/run_ilastik.sh"  # "/data/tathey1/matt_wright/ilastik/ilastik-1.4.0rc5-Linux/run_ilastik.sh"  # path to ilastik executable
 ilastik_project = (
-    brainline_exp_dir / "data" / "models" / "axon" / "axon_segmentation.ilp"
+    brainline_exp_dir / "data" / "validation-and-models" / "axon" / "axon_segmentation.ilp"
 )  # "/data/tathey1/matt_wright/ilastik/model1/axon_segmentation.ilp"  # path to ilastik
 ilastik_path = "/home/user/Documents/ilastik-1.4.0-Linux/run_ilastik.sh"
 
 
 min_coords = [
-    -1,
+    1024,
     -1,
     -1,
 ]  # max coords or -1 if you want to process everything along that dimension

diff --git a/experiments/BrainLine/scripts/soma_detect_image.py b/experiments/BrainLine/scripts/soma_detect_image.py
@@ -9,7 +9,8 @@
 # -dir_base
 # data_dir and results_dir ARE CLEAR
 # threshold IS CORRECT
-brain = "1252B"
+brain = "274L"
+
 antibody_layer = "Ch_647"
 background_layer = "Ch_561"
 endogenous_layer = "Ch_488"
@@ -25,11 +26,9 @@
 data_file = brainline_exp_dir / "data" / "soma_data.json"
 
 # Ilastik will run in "headless mode", and the following paths are needed to do so:
-ilastik_path = "/Applications/ilastik-1.4.0b21-OSX.app/Contents/ilastik-release/run_ilastik.sh"  # "/data/tathey1/matt_wright/ilastik/ilastik-1.4.0rc5-Linux/run_ilastik.sh"  # path to ilastik executable
-ilastik_project = "/Users/thomasathey/Documents/mimlab/mouselight/ailey/detection_soma/matt_soma_rabies_pix_3ch.ilp"  # "/data/tathey1/matt_wright/ilastik/soma_model/matt_soma_rabies_pix_3ch.ilp"  # path to ilastik project
 ilastik_path = "/home/user/Documents/ilastik-1.4.0-Linux/run_ilastik.sh"
 ilastik_project = (
-    brainline_exp_dir / "data" / "models" / "soma" / "matt_soma_rabies_pix_3ch.ilp"
+    brainline_exp_dir / "data" / "validation-and-models" / "soma" / "matt_soma_rabies_pix_3ch.ilp"
 )
 
 
@@ -39,11 +38,11 @@
     -1,
 ]  # max coords or -1 if you want to process everything along that dimension
 max_coords = [
-    6097,
-    11000,
+    6144,
+    -1,
     -1,
 ]  # max coords or -1 if you want to process everything along that dimension
-ncpu = 3  # 16  # number of cores to use for detection
+ncpu = 2  # 16  # number of cores to use for detection
 chunk_size = [1024, 1024, 1024]  # [256, 256, 300]
 
 """ 

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