diff --git a/src/synthesis_workflow/tasks/synthesis.py b/src/synthesis_workflow/tasks/synthesis.py
index 2a4e288..6023d35 100644
--- a/src/synthesis_workflow/tasks/synthesis.py
+++ b/src/synthesis_workflow/tasks/synthesis.py
@@ -34,6 +34,7 @@
 from synthesis_workflow.tasks.luigi_tools import ParamLink
 from synthesis_workflow.tasks.luigi_tools import RatioParameter
 from synthesis_workflow.tasks.luigi_tools import WorkflowTask
+from synthesis_workflow.tasks.utils import CreateAnnotationsFile
 from synthesis_workflow.tasks.utils import GetSynthesisInputs
 from synthesis_workflow.tools import ensure_dir
 from synthesis_workflow.tools import find_case_insensitive_file
@@ -323,19 +324,30 @@ def requires(self):
 
     def run(self):
         """"""
-
         ensure_dir(self.output().path)
         if self.annotations_path is None:
+            annotations_file = None
             neurondb_path = None
             atlas_path = None
             axon_cells = self.input()["axon_cells"].path
         else:
+            if Path(self.annotations_path).is_dir():
+                annotations_file = SynthesisLocalTarget("annotations.json").ppath
+                yield CreateAnnotationsFile(
+                    annotation_dir=self.annotations_path,
+                    destination=annotations_file,
+                )
+            else:
+                annotations_file = (
+                    Path(PathConfig().local_synthesis_input_path)
+                    / self.annotations_path
+                )
             axon_cells = None
             neurondb_path = find_case_insensitive_file(self.get_neuron_db_path("dat"))
 
         if any(
             [
-                self.annotations_path is None,
+                annotations_file is None,
                 self.placement_rules_path is None,
                 neurondb_path is None,
                 axon_cells is not None,
@@ -349,7 +361,7 @@ def run(self):
             self.input()["circuit"].path,
             morphs_df_path=axon_cells,
             atlas_path=atlas_path,
-            annotations_path=self.annotations_path,
+            annotations_path=annotations_file,
             rules_path=self.placement_rules_path,
             morphdb_path=neurondb_path,
             alpha=self.placement_alpha,
diff --git a/src/synthesis_workflow/tasks/utils.py b/src/synthesis_workflow/tasks/utils.py
index 44d77e1..7968a7c 100644
--- a/src/synthesis_workflow/tasks/utils.py
+++ b/src/synthesis_workflow/tasks/utils.py
@@ -1,10 +1,12 @@
 """Utils luigi tasks."""
+import json
 import shutil
 from pathlib import Path
 from tempfile import TemporaryDirectory
 
 import luigi
 from git import Repo
+from placement_algorithm.app.compact_annotations import _collect_annotations
 
 from synthesis_workflow.tasks.config import PathConfig
 from synthesis_workflow.tasks.luigi_tools import OutputLocalTarget
@@ -75,3 +77,25 @@ def output(self):
         """"""
         # TODO: it would probably be better to have a specific target for each file
         return OutputLocalTarget(PathConfig().local_synthesis_input_path)
+
+
+class CreateAnnotationsFile(WorkflowTask):
+    """Task to compact annotations into a single JSON file."""
+
+    annotation_dir = luigi.Parameter(description=(":str: Path to annotations folder."))
+    morph_db = luigi.OptionalParameter(
+        default=None, description=":str: Path to MorphDB file."
+    )
+    destination = luigi.Parameter(description=":str: Path to output JSON file.")
+
+    def run(self):
+        """"""
+        # pylint: disable=protected-access
+        annotations = _collect_annotations(self.annotation_dir, self.morph_db)
+
+        with open(self.destination, "w") as f:
+            json.dump(annotations, f, indent=4, sort_keys=True)
+
+    def output(self):
+        """"""
+        return OutputLocalTarget(self.destination)
diff --git a/src/synthesis_workflow/tasks/workflows.py b/src/synthesis_workflow/tasks/workflows.py
index f191671..1911f2b 100644
--- a/src/synthesis_workflow/tasks/workflows.py
+++ b/src/synthesis_workflow/tasks/workflows.py
@@ -63,7 +63,7 @@ def requires(self):
         if self.with_morphology_validation_reports:
             tasks.append(MorphologyValidationReports())
         if self.with_score_matrix_reports:
-            tasks.append(PlotScoreMatrix())
+            tasks.append(PlotScoreMatrix(in_atlas=True))
         return tasks
 
 
diff --git a/tests/data/in_small_O1/out/validation/score_matrix_reports.pdf b/tests/data/in_small_O1/out/validation/score_matrix_reports.pdf
index ea07be1..5089b37 100644
Binary files a/tests/data/in_small_O1/out/validation/score_matrix_reports.pdf and b/tests/data/in_small_O1/out/validation/score_matrix_reports.pdf differ
diff --git a/tests/test_O1_workflow.py b/tests/test_O1_workflow.py
index 3475a02..1af1893 100644
--- a/tests/test_O1_workflow.py
+++ b/tests/test_O1_workflow.py
@@ -36,6 +36,5 @@ def test_ValidateSynthesis(small_O1_working_directory):
             "validation/morphology_validation_reports/validation_results.json": {
                 "kwargs": {"precision": 1}  # weird precision issue in CI
             },
-            "validation/score_matrix_reports.pdf": {"kwargs": {"threshold": 64.5}},
         },
     )