update watershed notebooks to set erosion_width = 1

vanvalenlab · Aug 12, 2019 · 4564044 · 4564044
1 parent 2202825
commit 4564044
Show file tree

Hide file tree

Showing 4 changed files with 4 additions and 4 deletions.
diff --git a/scripts/watershed/Watershed Transform 2D Fully Convolutional.ipynb b/scripts/watershed/Watershed Transform 2D Fully Convolutional.ipynb
@@ -150,7 +150,7 @@
     "# Transformation settings\n",
     "transform = 'watershed'\n",
     "distance_bins = 4\n",
-    "erosion_width = 0  # erode edges"
+    "erosion_width = 1  # erode edges, improves segmentation when cells are close"
    ]
   },
   {

diff --git a/scripts/watershed/Watershed Transform 2D Sample Based.ipynb b/scripts/watershed/Watershed Transform 2D Sample Based.ipynb
@@ -150,7 +150,7 @@
     "# Transformation settings\n",
     "transform = 'watershed'\n",
     "distance_bins = 4  # number of distance \"classes\"\n",
-    "erosion_width = 0  # erode edges"
+    "erosion_width = 1  # erode edges, improves segmentation when cells are close"
    ]
   },
   {

diff --git a/scripts/watershed/Watershed Transform 3D Fully Convolutional.ipynb b/scripts/watershed/Watershed Transform 3D Fully Convolutional.ipynb
@@ -151,7 +151,7 @@
     "# Transformation settings\n",
     "transform = 'watershed'\n",
     "distance_bins = 4  # number of distance classes\n",
-    "erosion_width = 0  # erode edges\n",
+    "erosion_width = 1  # erode edges, improves segmentation when cells are close\n",
     "\n",
     "# 3D Settings\n",
     "frames_per_batch = 3"

diff --git a/scripts/watershed/Watershed Transform 3D Sample Based.ipynb b/scripts/watershed/Watershed Transform 3D Sample Based.ipynb
@@ -146,7 +146,7 @@
     "# Transformation settings\n",
     "transform = 'watershed'\n",
     "distance_bins = 4  # number of distance classes\n",
-    "erosion_width = 0  # erode edges\n",
+    "erosion_width = 1  # erode edges, improves segmentation when cells are close\n",
     "\n",
     "# 3D Settings\n",
     "frames_per_batch = 3\n",