diff --git a/embodied_gen/data/convex_decomposer.py b/embodied_gen/data/convex_decomposer.py
index 648f72a..57af815 100644
--- a/embodied_gen/data/convex_decomposer.py
+++ b/embodied_gen/data/convex_decomposer.py
@@ -37,6 +37,7 @@ def decompose_convex_coacd(
     params: dict,
     verbose: bool = False,
     auto_scale: bool = True,
+    scale_factor: float = 1.0,
 ) -> None:
     coacd.set_log_level("info" if verbose else "warn")
 
@@ -53,6 +54,7 @@ def decompose_convex_coacd(
         rescale = visual_mesh_shape / convex_mesh_shape
         combined.vertices *= rescale
 
+    combined.vertices *= scale_factor
     combined.export(outfile)
 
 
@@ -71,6 +73,7 @@ def decompose_convex_mesh(
     merge: bool = True,
     seed: int = 0,
     auto_scale: bool = True,
+    scale_factor: float = 1.005,
     verbose: bool = False,
 ) -> str:
     """Decompose a mesh into convex parts using the CoACD algorithm."""
@@ -95,7 +98,9 @@ def decompose_convex_mesh(
     )
 
     try:
-        decompose_convex_coacd(filename, outfile, params, verbose, auto_scale)
+        decompose_convex_coacd(
+            filename, outfile, params, verbose, auto_scale, scale_factor
+        )
         if os.path.exists(outfile):
             return outfile
     except Exception as e:
@@ -106,7 +111,7 @@ def decompose_convex_mesh(
         try:
             params["preprocess_mode"] = "on"
             decompose_convex_coacd(
-                filename, outfile, params, verbose, auto_scale
+                filename, outfile, params, verbose, auto_scale, scale_factor
             )
             if os.path.exists(outfile):
                 return outfile
diff --git a/embodied_gen/envs/pick_embodiedgen.py b/embodied_gen/envs/pick_embodiedgen.py
index b8fde92..b654bcc 100644
--- a/embodied_gen/envs/pick_embodiedgen.py
+++ b/embodied_gen/envs/pick_embodiedgen.py
@@ -74,7 +74,9 @@ class PickEmbodiedGen(BaseEnv):
         layout_file = kwargs.pop("layout_file", None)
         replace_objs = kwargs.pop("replace_objs", True)
         self.enable_grasp = kwargs.pop("enable_grasp", False)
-        self.init_quat = kwargs.pop("init_quat", [0.7071, 0, 0, 0.7071])
+        self.init_3dgs_quat = kwargs.pop(
+            "init_3dgs_quat", [0.7071, 0, 0, 0.7071]
+        )
         # Add small offset in z-axis to avoid collision.
         self.objs_z_offset = kwargs.pop("objs_z_offset", 0.002)
         self.robot_z_offset = kwargs.pop("robot_z_offset", 0.002)
@@ -107,7 +109,7 @@ class PickEmbodiedGen(BaseEnv):
         self.bg_images = dict()
         if self.render_mode == "hybrid":
             self.bg_images = self.render_gs3d_images(
-                self.layouts, num_envs, self.init_quat
+                self.layouts, num_envs, self.init_3dgs_quat
             )
 
     @staticmethod
diff --git a/embodied_gen/models/layout.py b/embodied_gen/models/layout.py
index 97ea38b..c3e9f23 100644
--- a/embodied_gen/models/layout.py
+++ b/embodied_gen/models/layout.py
@@ -77,9 +77,9 @@ LAYOUT_DISASSEMBLE_PROMPT = f"""
     - {Scene3DItemEnum.MANIPULATED_OBJS} and {Scene3DItemEnum.DISTRACTOR_OBJS} must be common
         household or office items or furniture, not abstract concepts, not too small like needle.
     - If the input includes a plural or grouped object (e.g., "pens", "bottles", "plates", "fruit"),
-        you must decompose it into multiple individual instances (e.g., ["pen", "pen"], ["apple", "pear"]).
+        you must decompose it into multiple individual instances (e.g., ["pen1", "pen2"], ["apple", "pear"]).
     - Containers that hold objects (e.g., "bowl of apples", "box of tools") must
-        be separated into individual items (e.g., ["bowl", "apple", "apple"]).
+        be separated into individual items (e.g., ["bowl", "apple1", "apple2"]).
     - Do not include transparent objects such as "glass", "plastic", etc.
     - The output must be in compact JSON format and use Markdown syntax, just like the output in the example below.
 
@@ -170,7 +170,7 @@ LAYOUT_DISASSEMBLE_PROMPT = f"""
         "robot": "franka",
         "background": "office",
         "context": "table",
-        "manipulated_objs": ["pen", "pen", "grey bowl"],
+        "manipulated_objs": ["pen1", "pen2", "grey bowl"],
         "distractor_objs": ["notepad", "cup"]
     }}
     ```
diff --git a/embodied_gen/scripts/compose_layout.py b/embodied_gen/scripts/compose_layout.py
index 4875574..0dae279 100644
--- a/embodied_gen/scripts/compose_layout.py
+++ b/embodied_gen/scripts/compose_layout.py
@@ -16,6 +16,7 @@
 
 import json
 import os
+import shutil
 from dataclasses import dataclass
 
 import tyro
@@ -51,6 +52,12 @@ def entrypoint(**kwargs):
     out_layout_path = f"{output_dir}/layout.json"
 
     layout_info = bfs_placement(args.layout_path, seed=args.seed)
+    origin_dir = os.path.dirname(args.layout_path)
+    for key in layout_info.assets:
+        src = f"{origin_dir}/{layout_info.assets[key]}"
+        dst = f"{output_dir}/{layout_info.assets[key]}"
+        shutil.copytree(src, dst, dirs_exist_ok=True)
+
     with open(out_layout_path, "w") as f:
         json.dump(layout_info.to_dict(), f, indent=4)
 
diff --git a/embodied_gen/scripts/simulate_sapien.py b/embodied_gen/scripts/simulate_sapien.py
index f62c950..8f25c47 100644
--- a/embodied_gen/scripts/simulate_sapien.py
+++ b/embodied_gen/scripts/simulate_sapien.py
@@ -49,7 +49,7 @@ class SapienSimConfig:
     sim_freq: int = 200
     sim_step: int = 400
     z_offset: float = 0.004
-    init_quat: list[float] = field(
+    init_3dgs_quat: list[float] = field(
         default_factory=lambda: [0.7071, 0, 0, 0.7071]
     )  # xyzw
     device: str = "cuda"
@@ -137,7 +137,7 @@ def entrypoint(**kwargs):
     gs_path = f"{asset_root}/{layout_data.assets[bg_node]}/gs_model.ply"
     gs_model: GaussianOperator = GaussianOperator.load_from_ply(gs_path)
     x, y, z, qx, qy, qz, qw = layout_data.position[bg_node]
-    qx, qy, qz, qw = quaternion_multiply([qx, qy, qz, qw], cfg.init_quat)
+    qx, qy, qz, qw = quaternion_multiply([qx, qy, qz, qw], cfg.init_3dgs_quat)
     init_pose = torch.tensor([x, y, z, qx, qy, qz, qw])
     gs_model = gs_model.get_gaussians(instance_pose=init_pose)
 
diff --git a/embodied_gen/utils/geometry.py b/embodied_gen/utils/geometry.py
index b1059ea..c265db6 100644
--- a/embodied_gen/utils/geometry.py
+++ b/embodied_gen/utils/geometry.py
@@ -80,7 +80,7 @@ def pose_to_matrix(pose: list[float]) -> np.ndarray:
 
 
 def compute_xy_bbox(
-    vertices: np.ndarray, col_x: int = 0, col_y: int = 2
+    vertices: np.ndarray, col_x: int = 0, col_y: int = 1
 ) -> list[float]:
     x_vals = vertices[:, col_x]
     y_vals = vertices[:, col_y]
@@ -139,11 +139,14 @@ def compute_convex_hull_path(
     z_threshold: float = 0.05,
     interp_per_edge: int = 3,
     margin: float = -0.02,
+    x_axis: int = 0,
+    y_axis: int = 1,
+    z_axis: int = 2,
 ) -> Path:
     top_vertices = vertices[
-        vertices[:, 1] > vertices[:, 1].max() - z_threshold
+        vertices[:, z_axis] > vertices[:, z_axis].max() - z_threshold
     ]
-    top_xy = top_vertices[:, [0, 2]]
+    top_xy = top_vertices[:, [x_axis, y_axis]]
 
     if len(top_xy) < 3:
         raise ValueError("Not enough points to form a convex hull")
@@ -184,11 +187,11 @@ def all_corners_inside(hull: Path, box: list, threshold: int = 3) -> bool:
 def compute_axis_rotation_quat(
     axis: Literal["x", "y", "z"], angle_rad: float
 ) -> list[float]:
-    if axis.lower() == 'x':
+    if axis.lower() == "x":
         q = Quaternion(axis=[1, 0, 0], angle=angle_rad)
-    elif axis.lower() == 'y':
+    elif axis.lower() == "y":
         q = Quaternion(axis=[0, 1, 0], angle=angle_rad)
-    elif axis.lower() == 'z':
+    elif axis.lower() == "z":
         q = Quaternion(axis=[0, 0, 1], angle=angle_rad)
     else:
         raise ValueError(f"Unsupported axis '{axis}', must be one of x, y, z")
@@ -226,12 +229,34 @@ def bfs_placement(
     floor_margin: float = 0,
     beside_margin: float = 0.1,
     max_attempts: int = 3000,
+    init_rpy: tuple = (1.5708, 0.0, 0.0),
     rotate_objs: bool = True,
     rotate_bg: bool = True,
+    rotate_context: bool = True,
     limit_reach_range: bool = True,
     robot_dim: float = 0.12,
     seed: int = None,
 ) -> LayoutInfo:
+    """Place objects in the layout using BFS traversal.
+
+    Args:
+        layout_file: Path to the JSON file defining the layout structure and assets.
+        floor_margin: Z-offset for the background object, typically for objects placed on the floor.
+        beside_margin: Minimum margin for objects placed 'beside' their parent, used when 'on' placement fails.
+        max_attempts: Maximum number of attempts to find a non-overlapping position for an object.
+        init_rpy: Initial Roll-Pitch-Yaw rotation rad applied to all object meshes to align the mesh's
+            coordinate system with the world's (e.g., Z-up).
+        rotate_objs: If True, apply a random rotation around the Z-axis for manipulated and distractor objects.
+        rotate_bg: If True, apply a random rotation around the Y-axis for the background object.
+        rotate_context: If True, apply a random rotation around the Z-axis for the context object.
+        limit_reach_range: If True, enforce a check that manipulated objects are within the robot's reach.
+        robot_dim: The approximate dimension (e.g., diameter) of the robot for box representation.
+        seed: Random seed for reproducible placement.
+
+    Returns:
+        A :class:`LayoutInfo` object containing the objects and their final computed 7D poses
+        ([x, y, z, qx, qy, qz, qw]).
+    """
     layout_info = LayoutInfo.from_dict(json.load(open(layout_file, "r")))
     asset_dir = os.path.dirname(layout_file)
     object_mapping = layout_info.objs_mapping
@@ -259,13 +284,23 @@ def bfs_placement(
         mesh_path = os.path.join(asset_dir, mesh_path)
         mesh_info[node]["path"] = mesh_path
         mesh = trimesh.load(mesh_path)
-        vertices = mesh.vertices
-        z1 = np.percentile(vertices[:, 1], 1)
-        z2 = np.percentile(vertices[:, 1], 99)
+        rotation = R.from_euler("xyz", init_rpy, degrees=False)
+        vertices = mesh.vertices @ rotation.as_matrix().T
+        z1 = np.percentile(vertices[:, 2], 1)
+        z2 = np.percentile(vertices[:, 2], 99)
 
         if object_mapping[node] == Scene3DItemEnum.CONTEXT.value:
             object_quat = [0, 0, 0, 1]
+            if rotate_context:
+                angle_rad = np.random.uniform(0, 2 * np.pi)
+                object_quat = compute_axis_rotation_quat(
+                    axis="z", angle_rad=angle_rad
+                )
+                rotation = R.from_quat(object_quat).as_matrix()
+                vertices = vertices @ rotation.T
+
             mesh_info[node]["surface"] = compute_convex_hull_path(vertices)
+
             # Put robot in the CONTEXT edge.
             x, y = random.choice(mesh_info[node]["surface"].vertices)
             theta = np.arctan2(y, x)
@@ -288,9 +323,7 @@ def bfs_placement(
                 axis="z", angle_rad=angle_rad
             )
             rotation = R.from_quat(object_quat).as_matrix()
-            vertices = np.dot(mesh.vertices, rotation.T)
-            z1 = np.percentile(vertices[:, 1], 1)
-            z2 = np.percentile(vertices[:, 1], 99)
+            vertices = vertices @ rotation.T
 
         x1, x2, y1, y2 = compute_xy_bbox(vertices)
         mesh_info[node]["pose"] = [x1, x2, y1, y2, z1, z2, *object_quat]
diff --git a/embodied_gen/validators/quality_checkers.py b/embodied_gen/validators/quality_checkers.py
index d7642c4..e289310 100644
--- a/embodied_gen/validators/quality_checkers.py
+++ b/embodied_gen/validators/quality_checkers.py
@@ -552,9 +552,8 @@ class SemanticMatcher(BaseChecker):
 
 
 def test_semantic_matcher(
-    bg_file: str = "outputs/bg_scenes/bg_scene_list.txt",
+    bg_file: str = "outputs/bg_scenes/scene_list.txt",
 ):
-    bg_file = "outputs/bg_scenes/bg_scene_list.txt"
     scene_dict = {}
     with open(bg_file, "r") as f:
         for line in f:
diff --git a/tests/test_integration/test_pipeline.sh b/tests/test_integration/test_pipeline.sh
index 12cca6f..7135723 100644
--- a/tests/test_integration/test_pipeline.sh
+++ b/tests/test_integration/test_pipeline.sh
@@ -23,3 +23,7 @@ layout-cli --task_descs "Place the pen in the mug on the desk" \
 --bg_list "outputs/bg_scenes/scene_list.txt" \
 --output_root "${output_dir}/layouts_gen" --insert_robot
 
+
+python embodied_gen/scripts/compose_layout.py \
+--layout_path "outputs/layouts_gen/task_0000/layout.json" \
+--output_dir "outputs/layouts_gen/task_0000/recompose" --insert_robot
\ No newline at end of file