segment.threshold: add option of gaussian filtering

README.md

@@ -44,6 +44,7 @@ process:  # choose method how to segment, filter, and sample the objects
 threshold:
     threshold: 128
     include_holes: yes
+    gaussian_sigma: 2.0 # optional 
 bounding_box:
     min_x: 64
     min_y: 0

src/faim_wako_searchfirst/segment.py

@@ -15,13 +15,15 @@
 import numpy as np
 from cellpose import models
 from scipy.ndimage import binary_fill_holes
+from skimage.filters import gaussian
 from skimage.measure import label, regionprops
 
 
 def threshold(
     img,
     threshold: int,
     include_holes: bool,
+    gaussian_sigma: float = 0.0,
     logger=logging,
 ):
     """Segment a given image by global thresholding.
@@ -33,6 +35,8 @@ def threshold(
 
     :return: a label image representing the detected objects
     """
+    if gaussian_sigma > 0:
+        img = gaussian(img, sigma=gaussian_sigma, preserve_range=True)
     mask = img > threshold
     if include_holes:
         mask = binary_fill_holes(mask)

tests/test_main.py

@@ -55,6 +55,15 @@ def test_partial(_image, tmp_path):
     )
     assert np.max(labels) == 7
 
+    # segment with gaussian
+    labels_blurred: np.ndarray = threshold(
+        _image,
+        threshold=128,
+        include_holes=True,
+        gaussian_sigma=5.5,
+    )
+    assert np.max(labels_blurred) == 4
+
     # filter
     label2 = labels.copy()
     bounding_box(