diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
index ac92e65..03f6c3e 100644
--- a/workflow/rules/common.smk
+++ b/workflow/rules/common.smk
@@ -9,6 +9,10 @@ IMAGE = f"{WORK}/image.zarr"
 IMAGE_OK = f"{IMAGE}/zarr.json"
 TILES = f"{WORK}/tiles.json"
 STAGE = f"{WORK}/stage.zarr"
+# Completion sentinel for the stage store. Tracking a touch()ed marker instead
+# of directory(STAGE) keeps Snakemake from deleting/recreating the store on a
+# re-run and avoids directory-mtime quirks (same touch() discipline as sopa).
+STAGE_OK = f"{STAGE}.done"
 
 
 def occupied_done(wildcards):
diff --git a/workflow/rules/segment.smk b/workflow/rules/segment.smk
index 3d3328f..2111868 100644
--- a/workflow/rules/segment.smk
+++ b/workflow/rules/segment.smk
@@ -5,7 +5,7 @@ checkpoint prepare:
         IMAGE_OK,
     output:
         tiles=TILES,
-        stage=directory(STAGE),
+        stage=touch(STAGE_OK),
     script:
         "../scripts/prepare_tiles.py"
 
@@ -14,7 +14,7 @@ rule segment:
     """Segment one tile on a GPU and write it into the stage store."""
     input:
         tiles=TILES,
-        stage=STAGE,
+        stage=STAGE_OK,
         image=IMAGE_OK,
     output:
         f"{WORK}/seg/{{index}}.done",