diff --git a/src/openflexure_microscope_server/utilities.py b/src/openflexure_microscope_server/utilities.py
index c93bf6ed..c4b328d4 100644
--- a/src/openflexure_microscope_server/utilities.py
+++ b/src/openflexure_microscope_server/utilities.py
@@ -137,9 +137,23 @@ def make_path_safe(unsafe_path_string: str) -> str:
         else _POSIX_UNSAFE_PATTERN
     )
 
-    for component in components:
+    for i, component in enumerate(components):
         if component in ("/", "\\"):
             sanitised_components.append(component)
+        elif component == ".":
+            # Only allow '.' if its the very first
+            # element and the next element is a separator.
+            # This allows for relative paths like "./file"
+            # but not "file./file"
+            is_first = i == 0
+            next_to_sep = (i + 1 < len(components)) and (
+                components[i + 1] in ("/", "\\")
+            )
+
+            if is_first and next_to_sep:
+                sanitised_components.append(component)
+            else:
+                sanitised_components.append("_")
         elif component:
             # 1. Strip trailing dots and spaces
             # 2. Apply unsafe character regex
diff --git a/tests/unit_tests/test_utilities.py b/tests/unit_tests/test_utilities.py
index 52f17c3f..84c25dc3 100644
--- a/tests/unit_tests/test_utilities.py
+++ b/tests/unit_tests/test_utilities.py
@@ -79,8 +79,30 @@ def test_make_path_safe_trailing_in_components():
     assert make_path_safe("path /to. /file ") == "path/to/file"
     assert make_path_safe("path./to /file.") == "path/to/file"
 
+    # Allow dots at the start of the path
+    # As this is common for hidden files on POSIX and relative paths
+    # And is the configuration in the manual and simulation config
+    # json files.
+    assert make_path_safe("./path/to/file") == "./path/to/file"
+    assert make_path_safe("./path./to /file.") == "./path/to/file"
+    assert make_path_safe("./openflexure/data/") == "./openflexure/data/"
+
 
 def test_make_path_safe_separators():
     """Test that separators are preserved and components sanitised."""
     assert make_path_safe("a/b\\c") == "a/b\\c"
     assert make_path_safe("a./b /c.") == "a/b/c"
+
+
+def test_make_path_safe_relative():
+    """Test that relative path components are preserved.
+    We only allow relative paths with one dot, and at the beginning of the path,
+    to avoid issues with paths like "file./file" or "file../file
+    """
+    assert make_path_safe("./openflexure/data/") == "./openflexure/data/"
+
+    assert make_path_safe("../openflexure/data/") == "_/openflexure/data/"
+    assert make_path_safe("path/./to/file") == "path/_/to/file"
+    assert make_path_safe("path/../to/file") == "path/_/to/file"
+    assert make_path_safe(".") == "_"
+    assert make_path_safe("..") == "_"