diff --git a/glotaran/analysis/problem_ungrouped.py b/glotaran/analysis/problem_ungrouped.py
index 32ee4c58e..38a8d522b 100644
--- a/glotaran/analysis/problem_ungrouped.py
+++ b/glotaran/analysis/problem_ungrouped.py
@@ -207,7 +207,7 @@ def _add_index_dependent_matrix_to_dataset(self, label: str, dataset: xr.Dataset
                 (model_dimension),
                 ("clp_label"),
             ),
-            matrix,
+            matrix.data,
         )
 
     def _add_index_independent_matrix_to_dataset(self, label: str, dataset: xr.Dataset):
@@ -218,7 +218,7 @@ def _add_index_independent_matrix_to_dataset(self, label: str, dataset: xr.Datas
                 (model_dimension),
                 ("clp_label"),
             ),
-            self.matrices[label],
+            self.matrices[label].data,
         )
 
     def _add_residual_and_full_clp_to_dataset(self, label: str, dataset: xr.Dataset):
@@ -230,14 +230,14 @@ def _add_residual_and_full_clp_to_dataset(self, label: str, dataset: xr.Dataset)
                 (model_dimension),
                 (global_dimension),
             ),
-            xr.concat(self.weighted_residuals[label], dim=global_dimension).T,
+            xr.concat(self.weighted_residuals[label], dim=global_dimension).T.data,
         )
         dataset["residual"] = (
             (
                 (model_dimension),
                 (global_dimension),
             ),
-            xr.concat(self.residuals[label], dim=global_dimension).T,
+            xr.concat(self.residuals[label], dim=global_dimension).T.data,
         )
 
     @property
diff --git a/glotaran/analysis/simulation.py b/glotaran/analysis/simulation.py
index 6edf40e67..c8efb3492 100644
--- a/glotaran/analysis/simulation.py
+++ b/glotaran/analysis/simulation.py
@@ -63,8 +63,8 @@ def simulate(
     result = xr.DataArray(
         data=0.0,
         coords=[
-            (model_dimension, model_axis),
-            (global_dimension, global_axis),
+            (model_dimension, model_axis.data),
+            (global_dimension, global_axis.data),
         ],
     )
     result = result.to_dataset(name="data")
diff --git a/glotaran/analysis/test/models.py b/glotaran/analysis/test/models.py
index a0dc47709..5d9d409b1 100644
--- a/glotaran/analysis/test/models.py
+++ b/glotaran/analysis/test/models.py
@@ -43,7 +43,7 @@ def calculate_matrix(self, dataset_model, indices, **kwargs):
             r_compartments.append(compartments[i])
             for j in range(axis.shape[0]):
                 array[j, i] = (i + j) * axis[j]
-        return xr.DataArray(array, coords=(("c", axis), ("clp_label", r_compartments)))
+        return xr.DataArray(array, coords=(("c", axis.data), ("clp_label", r_compartments)))
 
     def index_dependent(self, dataset_model):
         return self.is_index_dependent
@@ -75,7 +75,7 @@ def calculate_matrix(self, dataset_model, indices, **kwargs):
         else:
             compartments = [f"s{i+1}" for i in range(len(kinpar))]
         array = np.exp(np.outer(axis, kinpar))
-        return xr.DataArray(array, coords=(("c", axis), ("clp_label", compartments)))
+        return xr.DataArray(array, coords=(("c", axis.data), ("clp_label", compartments)))
 
     def index_dependent(self, dataset_model):
         return self.is_index_dependent
diff --git a/glotaran/builtin/models/kinetic_image/kinetic_baseline_megacomplex.py b/glotaran/builtin/models/kinetic_image/kinetic_baseline_megacomplex.py
index b6af03aac..4021cb0b5 100644
--- a/glotaran/builtin/models/kinetic_image/kinetic_baseline_megacomplex.py
+++ b/glotaran/builtin/models/kinetic_image/kinetic_baseline_megacomplex.py
@@ -22,7 +22,7 @@ def calculate_matrix(
         compartments = [f"{dataset_model.label}_baseline"]
         matrix = np.ones((model_axis.size, 1), dtype=np.float64)
         return xr.DataArray(
-            matrix, coords=((model_dimension, model_axis), ("clp_label", compartments))
+            matrix, coords=((model_dimension, model_axis.data), ("clp_label", compartments))
         )
 
     def index_dependent(self, dataset: DatasetDescriptor) -> bool:
diff --git a/glotaran/builtin/models/spectral/spectral_megacomplex.py b/glotaran/builtin/models/spectral/spectral_megacomplex.py
index a59fb65a0..7e3603552 100644
--- a/glotaran/builtin/models/spectral/spectral_megacomplex.py
+++ b/glotaran/builtin/models/spectral/spectral_megacomplex.py
@@ -41,7 +41,7 @@ def calculate_matrix(
         for i, shape in enumerate(self.shape.values()):
             matrix[:, i] += shape.calculate(model_axis.values)
         return xr.DataArray(
-            matrix, coords=((model_dimension, model_axis), ("clp_label", compartments))
+            matrix, coords=((model_dimension, model_axis.data), ("clp_label", compartments))
         )
 
     def index_dependent(self, dataset: DatasetDescriptor) -> bool:
diff --git a/tox.ini b/tox.ini
index b769ec467..6fe9c651c 100644
--- a/tox.ini
+++ b/tox.ini
@@ -8,6 +8,10 @@ envlist = py{38}, pre-commit, docs, docs-notebooks, docs-links
 ; Uncomment the following lines to deactivate pyglotaran all plugins
 ; env =
 ;     DEACTIVATE_GTA_PLUGINS=1
+; Uncomment to ignore deprecation warnings coming from pyglotaran
+; (this helps to see the warnings from dependencies)
+; filterwarnings =
+;     ignore:.+glotaran:DeprecationWarning
 
 [flake8]
 extend-ignore = E231, E203