diff --git a/src/Autoload/Tools.gd b/src/Autoload/Tools.gd
index 9e7f379d5..ec1861443 100644
--- a/src/Autoload/Tools.gd
+++ b/src/Autoload/Tools.gd
@@ -59,7 +59,7 @@ var shift := false
 var alt := false
 
 
-func _ready():
+func _ready() -> void:
 	yield(get_tree(), "idle_frame")
 	_slots[BUTTON_LEFT] = Slot.new("Left tool")
 	_slots[BUTTON_RIGHT] = Slot.new("Right tool")
@@ -72,9 +72,9 @@ func _ready():
 	value = Global.config_cache.get_value(_slots[BUTTON_RIGHT].kname, "tool", "Eraser")
 	set_tool(value, BUTTON_RIGHT)
 	value = Global.config_cache.get_value(_slots[BUTTON_LEFT].kname, "color", Color.black)
-	assign_color(value, BUTTON_LEFT)
+	assign_color(value, BUTTON_LEFT, false)
 	value = Global.config_cache.get_value(_slots[BUTTON_RIGHT].kname, "color", Color.white)
-	assign_color(value, BUTTON_RIGHT)
+	assign_color(value, BUTTON_RIGHT, false)
 
 	update_tool_buttons()
 	update_tool_cursors()
@@ -115,13 +115,14 @@ func default_color() -> void:
 func swap_color() -> void:
 	var left = _slots[BUTTON_LEFT].color
 	var right = _slots[BUTTON_RIGHT].color
-	assign_color(right, BUTTON_LEFT)
-	assign_color(left, BUTTON_RIGHT)
+	assign_color(right, BUTTON_LEFT, false)
+	assign_color(left, BUTTON_RIGHT, false)
 
 
-func assign_color(color : Color, button : int) -> void:
+func assign_color(color : Color, button : int, change_alpha := true) -> void:
 	var c : Color = _slots[button].color
-	if color.a == 0:
+	# This was requested by Issue #54 on GitHub
+	if color.a == 0 and change_alpha:
 		if color.r != c.r or color.g != c.g or color.b != c.b:
 			color.a = 1
 	_slots[button].color = color
diff --git a/src/Palette/PaletteContainer.gd b/src/Palette/PaletteContainer.gd
index c2058614f..abe3e0df6 100644
--- a/src/Palette/PaletteContainer.gd
+++ b/src/Palette/PaletteContainer.gd
@@ -268,9 +268,9 @@ func on_color_select(index : int) -> void:
 	var color : Color = Global.palettes[current_palette].get_color(index)
 
 	if Input.is_action_just_pressed("left_mouse"):
-		Tools.assign_color(color, BUTTON_LEFT)
+		Tools.assign_color(color, BUTTON_LEFT, false)
 	elif Input.is_action_just_pressed("right_mouse"):
-		Tools.assign_color(color, BUTTON_RIGHT)
+		Tools.assign_color(color, BUTTON_RIGHT, false)
 
 
 func _load_palettes() -> void:
diff --git a/src/Tools/ColorPicker.gd b/src/Tools/ColorPicker.gd
index 36596e2be..45866fc29 100644
--- a/src/Tools/ColorPicker.gd
+++ b/src/Tools/ColorPicker.gd
@@ -48,4 +48,4 @@ func _pick_color(position : Vector2) -> void:
 	image.lock()
 	var color := image.get_pixelv(position)
 	var button := BUTTON_LEFT if _color_slot == 0 else BUTTON_RIGHT
-	Tools.assign_color(color, button)
+	Tools.assign_color(color, button, false)