diff --git a/src/file_handler.py b/src/file_handler.py
index 16b7da62e87666fbb47315bfc49248637118f44b..6441edb3781b79d98cff9e8e8504293b2a63bc33 100644
--- a/src/file_handler.py
+++ b/src/file_handler.py
@@ -166,6 +166,7 @@ def parse_input():
     tomogram = read_mrc(user_inputs["tomogram"])
     if not user_inputs['black_on_white']:
         tomogram = -tomogram
+        print("Inverted the tomogram contrast to match template.")
     dims = tomogram.shape
     templates = [read_mrc_permissive(template) for template in user_inputs["templates"]]
     if user_inputs["masks"]:
diff --git a/test/s68/catm/config.py b/test/s68/catm/config.py
index f362bdb58af78ac2d9c8f9445ec4d54fea7828e2..843fcebba7bb21bb75e31cfaa3100c1cc920839b 100644
--- a/test/s68/catm/config.py
+++ b/test/s68/catm/config.py
@@ -19,7 +19,7 @@ tomoID = split_path[-2]
 prefix = tomoID + ".test1.catm"
 input_folder = "inputs/"
 tomogram = input_folder + tomoID + ".test1.lps25.mrc"
-
+black_on_white = 1 # The contrast of tomogram, 0 if the particle has white contrast (positive values)
 templates = [input_folder + "mono-8Apx-lps30-box30-rot12-core.mrc"]
 contour_level = [0.2]
 #  Masks are required to be the same shape as the templates
diff --git a/test/s68/tm/config.py b/test/s68/tm/config.py
index 2fa7604e6d88b8e1b63c47b24de3f4f198e9bb76..046548bfffa782b5acfce7bb87a464e888400898 100644
--- a/test/s68/tm/config.py
+++ b/test/s68/tm/config.py
@@ -19,6 +19,7 @@ tomoID = split_path[-2]
 prefix = tomoID + ".test1"
 input_folder = "inputs/"
 tomogram = input_folder + tomoID + ".test1.lps25.mrc"
+black_on_white = 1 # The contrast of tomogram, 0 if the particle has white contrast (positive values)
 
 templates = [input_folder + "mono-8Apx-lps30-box30-rot12-core.mrc"]
 contour_level = [0.2]