diff --git a/src/aspire/source/micrograph.py b/src/aspire/source/micrograph.py
index e6c8e6a3b..a0e11e61a 100644
--- a/src/aspire/source/micrograph.py
+++ b/src/aspire/source/micrograph.py
@@ -402,10 +402,18 @@ def __init__(
                     f" {acceptable_lens[1]}, or {acceptable_lens[2]}."
                 )
 
-            # Generate explicit filter indices (zero-indexed).
-            self.filter_indices = np.arange(self.total_particle_count) % len(
-                ctf_filters
-            )
+            # Generate explicit total_particle_count filter_indices
+            # Note these indices are zero-indexed.
+            if len(ctf_filters) == self.micrograph_count:
+                # creates mapping [0,0,0..., 1,1,1,... ,micrograph_count-1]
+                self.filter_indices = np.repeat(
+                    np.arange(self.micrograph_count, dtype=int),
+                    self.particles_per_micrograph,
+                )
+            elif len(ctf_filters) == self.total_particle_count:
+                self.filter_indices = np.arange(self.total_particle_count, dtype=int)
+            elif len(ctf_filters) == 1:
+                self.filter_indices = np.zeros(self.total_particle_count, dtype=int)
 
         self.ctf_filters = ctf_filters