diff --git a/tools/2d_auto_threshold/auto_threshold.py b/tools/2d_auto_threshold/auto_threshold.py
index 428547e7..4eec3297 100644
--- a/tools/2d_auto_threshold/auto_threshold.py
+++ b/tools/2d_auto_threshold/auto_threshold.py
@@ -7,12 +7,14 @@
 
 import argparse
 
+import giatools
 import numpy as np
 import skimage.filters
 import skimage.io
 import skimage.util
 import tifffile
 
+
 th_methods = {
     'manual': lambda thres, **kwargs: thres,
 
@@ -28,7 +30,7 @@
 
 
 def do_thresholding(in_fn, out_fn, th_method, block_size, offset, threshold, invert_output=False):
-    img = skimage.io.imread(in_fn)
+    img = giatools.imread(in_fn)
     img = np.squeeze(img)
     assert img.ndim == 2
 
diff --git a/tools/2d_auto_threshold/auto_threshold.xml b/tools/2d_auto_threshold/auto_threshold.xml
index 20042c52..9206b3a7 100644
--- a/tools/2d_auto_threshold/auto_threshold.xml
+++ b/tools/2d_auto_threshold/auto_threshold.xml
@@ -4,7 +4,7 @@
         <import>creators.xml</import>
         <import>tests.xml</import>
         <token name="@TOOL_VERSION@">0.18.1</token>
-        <token name="@VERSION_SUFFIX@">2</token>
+        <token name="@VERSION_SUFFIX@">3</token>
         <xml name="inputs/offset">
             <param name="offset" type="float" value="0" label="Offset" help="Offset to be added to the automatically determined threshold value. Positive values will increase the threshold (and thus reduce the amount of values above the threshold)." />
         </xml>
diff --git a/tools/2d_auto_threshold/giatools.py b/tools/2d_auto_threshold/giatools.py
new file mode 100644
index 00000000..db6a543c
--- /dev/null
+++ b/tools/2d_auto_threshold/giatools.py
@@ -0,0 +1,30 @@
+"""
+Copyright 2017-2024 Leonid Kostrykin, Biomedical Computer Vision Group, Heidelberg University.
+
+Distributed under the MIT license.
+See file LICENSE for detail or copy at https://opensource.org/licenses/MIT
+"""
+
+import contextlib
+
+import skimage.io
+
+
+def imread(*args, **kwargs):
+    """
+    Wrapper around ``skimage.io.imread`` which mutes non-fatal errors.
+
+    When using ``skimage.io.imread`` to read an image file, sometimes errors can be reported although the image file will be read successfully.
+    In those cases, Galaxy might detect the errors and assume that the tool has failed: https://docs.galaxyproject.org/en/latest/dev/schema.html#error-detection
+    To prevent this, this wrapper around ``skimage.io.imread`` will mute non-fatal all errors.
+    """
+    try:
+
+        # Mute stderr unless an error occurs
+        with contextlib.redirect_stderr(None):
+            return skimage.io.imread(*args, **kwargs)
+
+    except:  # noqa: E722
+
+        # Raise the error outside of the contextlib redirection
+        raise