diff --git a/containers/azimuth/context/main.py b/containers/azimuth/context/main.py
index e3a67f0..106b805 100644
--- a/containers/azimuth/context/main.py
+++ b/containers/azimuth/context/main.py
@@ -4,7 +4,9 @@
 from pathlib import Path
 
 import anndata
+import numpy as np
 import pandas
+import scipy.sparse as sp_sparse
 
 from src.algorithm import Algorithm, RunResult, add_common_arguments
 from src.util.layers import set_data_layer
@@ -41,8 +43,9 @@ def do_run(
         # after which the annotations are copied back to the original matrix
         temp_index = self.create_temp_obs_index(data)
         clean_matrix_path = Path("clean_matrix.h5ad")
-        clean_matrix = self.create_clean_matrix(data, temp_index)
-        clean_matrix = set_data_layer(clean_matrix, options["query_layers_key"])
+        clean_matrix = self.create_clean_matrix(
+            data, temp_index, options["query_layers_key"]
+        )
         clean_matrix.write_h5ad(clean_matrix_path)
 
         annotated_matrix_path = self.run_azimuth_scripts(
@@ -71,28 +74,34 @@ def create_temp_obs_index(self, matrix: anndata.AnnData) -> pandas.Index:
         return matrix.obs.index.map(lambda name: f"QUERY:{name}")
 
     def create_clean_matrix(
-        self,
-        matrix: anndata.AnnData,
-        temp_index: pandas.Index,
+        self, matrix: anndata.AnnData, temp_index: pandas.Index, layer: t.Optional[str]
     ) -> anndata.AnnData:
-        """Creates a copy of the data with all observation columns removed.
+        """Creates a copy of the data with all extra attributes removed.
 
         Args:
             matrix (anndata.AnnData): Original data
             temp_index (pandas.Index): Temporary index generated by `create_temp_obs_index`
+            layer (str | None): Data layer to use
 
         Returns:
             anndata.AnnData: Cleaned data
         """
         clean_obs = pandas.DataFrame(index=temp_index)
         clean_matrix = matrix.copy()
+        clean_matrix = set_data_layer(clean_matrix, layer)
         clean_matrix.obs = clean_obs
         clean_matrix.obsm = None
         clean_matrix.obsp = None
         clean_matrix.varm = None
         clean_matrix.varp = None
+        clean_matrix.raw = None
+        clean_matrix.layers = None
         clean_matrix.uns = {}
 
+        # Azimuth cannot properly load numpy arrays. Only csc and csr matrices
+        if isinstance(clean_matrix.X, np.ndarray):
+            clean_matrix.X = sp_sparse.csr_matrix(clean_matrix.X)
+
         return clean_matrix
 
     def copy_annotations(