Increase range of threshold sigma parameter (#134)

Addressing #131 with the proposed solution of creating a threshold proportional to the max value of the image
epitools · Sep 22, 2023 · 78b2623 · 78b2623
1 parent 3fabc06
commit 78b2623
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Showing 3 changed files with 8 additions and 3 deletions.
diff --git a/src/epitools/analysis/segmentation.py b/src/epitools/analysis/segmentation.py
@@ -52,7 +52,7 @@ def thresholded_local_minima_seeded_watershed(
     image: npt.NDArray[np.float64],
     spot_sigma: float = 3,
     outline_sigma: float = 0,
-    minimum_intensity: float = 500,
+    minimum_intensity: float = 0.01,
 ) -> tuple[list[list[Any]], npt.NDArray[np.uint32]]:
     """
     Segment cells in images with marked membranes that have a high signal intensity.
@@ -63,6 +63,7 @@ def thresholded_local_minima_seeded_watershed(
     Afterwards, all objects are removed that have an average intensity below a given
     minimum_intensity
     """
+
     spots, labels = local_minima_seeded_watershed(
         image, spot_sigma=spot_sigma, outline_sigma=outline_sigma
     )
@@ -75,6 +76,9 @@ def thresholded_local_minima_seeded_watershed(
     stats = regionprops(labels, image)
     intensities = [r.mean_intensity for r in stats]
 
+    # Normalise intensities based on the max
+    minimum_intensity = minimum_intensity * max(np.asarray(intensities))
+
     # filter labels with low intensity
     new_label_indices, _, _ = relabel_sequential(
         (np.asarray(intensities) > minimum_intensity) * np.arange(1, labels.max() + 1)

diff --git a/src/epitools/widgets/segmentation.py b/src/epitools/widgets/segmentation.py
@@ -41,12 +41,13 @@ def create_segmentation_widget() -> magicgui.widgets.Container:
 
     threshold_tooltip = "Cells with an average intensity below `threshold` are ignored."
     threshold = magicgui.widgets.create_widget(
-        value=3.0,
+        value=0.01,
         name="threshold",
         label="threshold sigma",
         widget_type="FloatSpinBox",
         options={
             "tooltip": threshold_tooltip,
+            "max": 1.0,
         },
     )
 

diff --git a/tests/test_segmentation.py b/tests/test_segmentation.py
@@ -12,7 +12,7 @@
 
 SPOT_SIGMA = 4.0
 OUTLINE_SIGMA = 3.0
-THRESHOLD = 3.0
+THRESHOLD = 0.04
 
 
 def test_add_segmentation_widget(