theislab · LeonStadelmann · Jun 15, 2025 · May 11, 2025 · May 11, 2025 · May 11, 2025
diff --git a/examples/problems/400_subset_policy.ipynb b/examples/problems/400_subset_policy.ipynb
@@ -15,7 +15,7 @@
     "{class}`~moscot.problems.time.TemporalProblem`, we can choose among different policies as demonstrated below.\n",
     "\n",
     ":::{seealso}\n",
-    "- See {doc}`AlignmentProblem/1300_sequential_alignment.ipynb` on how to use different policies in the {class}`~moscot.problems.space.AlignmentProblem`.\n",
+    "- See {doc}`AlignmentProblem/1300_sequential_alignment` on how to use different policies in the {class}`~moscot.problems.space.AlignmentProblem`.\n",
     ":::"
    ]
   },

diff --git a/examples/problems/AlignmentProblem/1300_sequential_alignment.ipynb b/examples/problems/AlignmentProblem/1300_sequential_alignment.ipynb
@@ -9,8 +9,8 @@
     "In this example we focus on how to use different policies in the {class}`~moscot.problems.space.AlignmentProblem` to produce specific alignments of spatial samples.\n",
     "\n",
     ":::{seealso}\n",
-    "- See {doc}`../400_subset_policy.ipynb` on how to use different policies.\n",
-    "- See {doc}`../../../tutorials/300_spatial_alignment.ipynb` on how to align spatial transcriptomics data.\n",
+    "- See {doc}`../400_subset_policy` on how to use different policies.\n",
+    "- See {doc}`../../../tutorials/300_spatial_alignment` on how to align spatial transcriptomics data.\n",
     ":::"
    ]
   },

diff --git a/examples/problems/AlignmentProblem/index.rst b/examples/problems/AlignmentProblem/index.rst
@@ -0,0 +1,8 @@
+Alignment Problem
+=================
+
+.. toctree::
+   :maxdepth: 1
+   :glob:
+
+   ./*
diff --git a/examples/problems/LineageProblem/index.rst b/examples/problems/LineageProblem/index.rst
@@ -0,0 +1,8 @@
+Lineage Problem
+================
+
+.. toctree::
+   :maxdepth: 1
+   :glob:
+
+   ./*
diff --git a/examples/problems/SpatioTemporalProblem/index.rst b/examples/problems/SpatioTemporalProblem/index.rst
@@ -0,0 +1,8 @@
+Spatio Temporal Problem
+=======================
+
+.. toctree::
+   :maxdepth: 1
+   :glob:
+
+   ./*
diff --git a/examples/problems/TemporalProblem/index.rst b/examples/problems/TemporalProblem/index.rst
@@ -0,0 +1,8 @@
+Temporal Problem
+================
+
+.. toctree::
+   :maxdepth: 1
+   :glob:
+
+   ./*
diff --git a/examples/problems/index.rst b/examples/problems/index.rst
@@ -0,0 +1,10 @@
+Problems
+========
+
+.. toctree::
+   :maxdepth: 1
+
+   AlignmentProblem/index
+   LineageProblem/index
+   SpatioTemporalProblem/index
+   TemporalProblem/index