From 3ca94fa31848bbf617ce66bbf3940acfe89c3b0b Mon Sep 17 00:00:00 2001
From: Laurent Guerard <laurent.guerard@unibas.ch>
Date: Tue, 31 Mar 2026 15:03:52 +0200
Subject: [PATCH 1/3] feat: Enhance rolling ball background subtraction with
 additional options

---
 src/imcflibs/imagej/processing.py | 28 ++++++++++++++++++++++++++--
 1 file changed, 26 insertions(+), 2 deletions(-)

diff --git a/src/imcflibs/imagej/processing.py b/src/imcflibs/imagej/processing.py
index 41a6b9ae..767e2a63 100644
--- a/src/imcflibs/imagej/processing.py
+++ b/src/imcflibs/imagej/processing.py
@@ -66,7 +66,14 @@ def apply_filter(imp, filter_method, filter_radius, do_3d=False):
     return imageplus
 
 
-def apply_rollingball_bg_subtraction(imp, rolling_ball_radius, do_3d=False):
+def apply_rollingball_bg_subtraction(
+    imp,
+    rolling_ball_radius,
+    light_background=False,
+    sliding=False,
+    disable=False,
+    do_3d=False,
+):
     """Perform background subtraction using a rolling ball method.
 
     Parameters
@@ -75,6 +82,12 @@ def apply_rollingball_bg_subtraction(imp, rolling_ball_radius, do_3d=False):
         Input ImagePlus to filter and threshold
     rolling_ball_radius : int
         Radius of the rolling ball filter to use
+    light_background : bool, optional
+        If set to True, will treat the background as light, by default False
+    sliding : bool, optional
+        If set to True, will do a sliding window approach, by default False
+    disable : bool, optional
+        If set to True, will disable the smoothing, by default False
     do_3d : bool, optional
         If set to True, will do a 3D filtering, by default False
 
@@ -85,7 +98,18 @@ def apply_rollingball_bg_subtraction(imp, rolling_ball_radius, do_3d=False):
     """
     log.info("Applying rolling ball with radius %d" % rolling_ball_radius)
 
-    options = "rolling=" + str(rolling_ball_radius) + " stack" if do_3d else ""
+    option_parts = ["rolling=" + str(rolling_ball_radius)]
+
+    if light_background:
+        option_parts.append("light")
+    if sliding:
+        option_parts.append("sliding")
+    if disable:
+        option_parts.append("disable")
+    if do_3d:
+        option_parts.append("stack")
+
+    options = " ".join(option_parts)
 
     log.debug("Background subtraction options: %s" % options)
 

From 6659e1188eeada0879dc5c9545d90603e769443f Mon Sep 17 00:00:00 2001
From: Laurent Guerard <laurent.guerard@unibas.ch>
Date: Tue, 31 Mar 2026 15:09:03 +0200
Subject: [PATCH 2/3] fix: Correct spelling of 'Subtract Background' in rolling
 ball background subtraction function

---
 src/imcflibs/imagej/processing.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/imcflibs/imagej/processing.py b/src/imcflibs/imagej/processing.py
index 767e2a63..910e865c 100644
--- a/src/imcflibs/imagej/processing.py
+++ b/src/imcflibs/imagej/processing.py
@@ -114,7 +114,7 @@ def apply_rollingball_bg_subtraction(
     log.debug("Background subtraction options: %s" % options)
 
     imageplus = imp.duplicate()
-    IJ.run(imageplus, "Substract Background...", options)
+    IJ.run(imageplus, "Subtract Background...", options)
 
     return imageplus
 

From cd48fac5743c3b748e96fde4b68d8cf2aa018791 Mon Sep 17 00:00:00 2001
From: Laurent Guerard <laurent.guerard@unibas.ch>
Date: Tue, 31 Mar 2026 15:19:15 +0200
Subject: [PATCH 3/3] refactor: Extract rolling ball options into a separate
 function for clarity

---
 src/imcflibs/imagej/processing.py | 39 +++++++++++++++++++++----------
 1 file changed, 27 insertions(+), 12 deletions(-)

diff --git a/src/imcflibs/imagej/processing.py b/src/imcflibs/imagej/processing.py
index 910e865c..0aa223c1 100644
--- a/src/imcflibs/imagej/processing.py
+++ b/src/imcflibs/imagej/processing.py
@@ -98,18 +98,13 @@ def apply_rollingball_bg_subtraction(
     """
     log.info("Applying rolling ball with radius %d" % rolling_ball_radius)
 
-    option_parts = ["rolling=" + str(rolling_ball_radius)]
-
-    if light_background:
-        option_parts.append("light")
-    if sliding:
-        option_parts.append("sliding")
-    if disable:
-        option_parts.append("disable")
-    if do_3d:
-        option_parts.append("stack")
-
-    options = " ".join(option_parts)
+    options = rolling_ball_options(
+        rolling_ball_radius,
+        light_background=light_background,
+        sliding=sliding,
+        disable=disable,
+        do_3d=do_3d,
+    )
 
     log.debug("Background subtraction options: %s" % options)
 
@@ -119,6 +114,26 @@ def apply_rollingball_bg_subtraction(
     return imageplus
 
 
+def rolling_ball_options(
+    rolling_ball_radius,
+    light_background=False,
+    sliding=False,
+    disable=False,
+    do_3d=False,
+):
+    """Return the option string for rolling ball background subtraction."""
+    parts = ["rolling=" + str(rolling_ball_radius)]
+    if light_background:
+        parts.append("light")
+    if sliding:
+        parts.append("sliding")
+    if disable:
+        parts.append("disable")
+    if do_3d:
+        parts.append("stack")
+    return " ".join(parts)
+
+
 def apply_threshold(imp, threshold_method, do_3d=True):
     """Apply a threshold method to the input ImagePlus.