diff --git a/examples/Notebook.ipynb b/examples/Notebook.ipynb
index d9c6488f..953143d8 100644
--- a/examples/Notebook.ipynb
+++ b/examples/Notebook.ipynb
@@ -187,6 +187,86 @@
     "\n",
     "doc"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "679bd8dd-9bbf-4ecf-a676-32e8137992d1",
+   "metadata": {},
+   "source": [
+    "#### Add annotations and modify shape color"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "id": "245baeb7-5df6-45a3-bd75-aa4a33258fce",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.ywidget-view+json": {
+       "model_id": "d5fc57c284414950ab29413d60e1a50a",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "<jupytercad.notebook.cad_document.CadDocument object at 0x7f0235f23a90>"
+      ]
+     },
+     "execution_count": 14,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "from OCC.Core.gp import gp_Pnt\n",
+    "\n",
+    "from jupytercad import CadDocument\n",
+    "\n",
+    "doc = CadDocument('test.jcad')\n",
+    "doc"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "id": "cf45ee1f-76ee-4973-818f-167ce82ea384",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "user= {'color':'#0000ff30', 'initials': 'BO','display_name': 'Bot'}\n",
+    "id = doc.add_annotation('box','Added from Python API', user=user)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 17,
+   "id": "08764533-d8f8-494f-8a59-9dd5360ba17e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "doc.remove_annotation(id)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 18,
+   "id": "3afc5f3c-cc33-4c8a-8904-98726a3ae118",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "doc.set_color('box2', [0.5,0.4,0.2])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "id": "855133ee-8cd2-432b-933a-d72f1a9f6c7c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "doc.set_color('box2',None)"
+   ]
   }
  ],
  "metadata": {
@@ -205,7 +285,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.10.10"
   }
  },
  "nbformat": 4,
diff --git a/jupytercad/fcstd_ydoc.py b/jupytercad/fcstd_ydoc.py
index c60b724e..b5b3eebf 100644
--- a/jupytercad/fcstd_ydoc.py
+++ b/jupytercad/fcstd_ydoc.py
@@ -60,7 +60,7 @@ def observe(self, callback: Callable[[str, Any], None]):
         self._subscriptions[self._yobjects] = self._yobjects.observe_deep(
             partial(callback, "objects")
         )
-        self._subscriptions[self._yoptions] = self._yoptions.observe(
+        self._subscriptions[self._yoptions] = self._yoptions.observe_deep(
             partial(callback, "options")
         )
         self._subscriptions[self._ymeta] = self._ymeta.observe_deep(
diff --git a/jupytercad/jcad_ydoc.py b/jupytercad/jcad_ydoc.py
index 09824ae7..bf93dc71 100644
--- a/jupytercad/jcad_ydoc.py
+++ b/jupytercad/jcad_ydoc.py
@@ -61,9 +61,9 @@ def observe(self, callback: Callable[[str, Any], None]):
         self._subscriptions[self._yobjects] = self._yobjects.observe_deep(
             partial(callback, "objects")
         )
-        self._subscriptions[self._yoptions] = self._yoptions.observe(
+        self._subscriptions[self._yoptions] = self._yoptions.observe_deep(
             partial(callback, "options")
         )
-        self._subscriptions[self._ymeta] = self._ymeta.observe(
+        self._subscriptions[self._ymeta] = self._ymeta.observe_deep(
             partial(callback, "meta")
         )
diff --git a/jupytercad/notebook/cad_document.py b/jupytercad/notebook/cad_document.py
index 347aef5e..828323c9 100644
--- a/jupytercad/notebook/cad_document.py
+++ b/jupytercad/notebook/cad_document.py
@@ -1,4 +1,5 @@
 from __future__ import annotations
+from copy import deepcopy
 
 import json
 import logging
@@ -12,6 +13,7 @@
 
 from jupytercad.freecad.loader import fc
 from jupytercad.notebook.objects._schema.any import IAny
+from uuid import uuid4
 
 from .objects import (
     IBox,
@@ -52,6 +54,8 @@ def __init__(self, path: Optional[str] = None):
         self.ydoc = ydoc
 
         self._objects_array = self.ydoc.get_array("objects")
+        self._metadata = self.ydoc.get_map("metadata")
+        self._options = self.ydoc.get_map("options")
 
     @property
     def objects(self) -> List[str]:
@@ -114,6 +118,86 @@ def add_object(self, new_object: "PythonJcadObject") -> CadDocument:
             logger.error(f"Object {new_object.name} already exists")
         return self
 
+    def add_annotation(
+        self,
+        parent: str,
+        message: str,
+        *,
+        position: Optional[List[float]] = None,
+        user: Optional[Dict] = None,
+    ) -> Optional[str]:
+        """
+        Add an annotation to the document.
+
+        :param parent: The object which holds the annotation.
+        :param message: The first messages in the annotation.
+        :param position: The position of the annotation.
+        :param user: The user who create this annotation.
+        :return: The id of the annotation if it is created.
+        """
+        new_id = f"annotation_${uuid4()}"
+        parent_obj = self.get_object(parent)
+        if parent_obj is None:
+            raise ValueError("Parent object not found")
+
+        if position is None:
+            position = (
+                parent_obj.metadata.centerOfMass
+                if parent_obj.metadata is not None
+                else [0, 0, 0]
+            )
+        contents = [{"user": user, "value": message}]
+        if self._metadata is not None:
+            with self.ydoc.begin_transaction() as t:
+                self._metadata.set(
+                    t,
+                    new_id,
+                    json.dumps(
+                        {
+                            "position": position,
+                            "contents": contents,
+                            "parent": parent,
+                        }
+                    ),
+                )
+            return new_id
+
+    def remove_annotation(self, annotation_id: str) -> None:
+        """
+        Remove an annotation from the document.
+
+        :param annotation_id: The id of the annotation
+        """
+        if self._metadata is not None:
+            with self.ydoc.begin_transaction() as t:
+                self._metadata.pop(t, annotation_id, None)
+
+    def set_color(self, object_name: str, color: Optional[List]) -> None:
+        """
+        Set object color.
+
+        :param object_name: Object name.
+        :param color: Color value, set it to `None` to remove color.
+        """
+        if self._options and self.check_exist(object_name):
+            current_gui = self._options.get("guidata")
+            new_gui = None
+            if current_gui is not None:
+                new_gui = deepcopy(current_gui)
+                current_data: Dict = new_gui.get(object_name, {})
+                if color is not None:
+                    current_data["color"] = color
+                else:
+                    current_data.pop("color", None)
+
+                new_gui[object_name] = current_data
+            else:
+                if color is not None:
+                    new_gui = {object_name: {"color": color}}
+            if new_gui is not None:
+                with self.ydoc.begin_transaction() as t:
+                    self._options.set(t, "guidata", new_gui)
+
     def add_occ_shape(
         self,
         shape,
diff --git a/packages/jupytercad-extension/src/mainview.tsx b/packages/jupytercad-extension/src/mainview.tsx
index 0496a284..c1434ea5 100644
--- a/packages/jupytercad-extension/src/mainview.tsx
+++ b/packages/jupytercad-extension/src/mainview.tsx
@@ -547,7 +547,6 @@ export class MainView extends React.Component<IProps, IStates> {
     }
 
     const guidata = this._model.sharedModel.getOption('guidata');
-
     const selectedNames = this._selectedMeshes.map(sel => sel.name);
     this._selectedMeshes = [];
 
@@ -932,15 +931,20 @@ export class MainView extends React.Component<IProps, IStates> {
 
     if (guidata) {
       for (const objName in guidata) {
+        const obj = this._meshGroup?.getObjectByName(objName) as
+          | BasicMesh
+          | undefined;
+        if (!obj) {
+          continue;
+        }
         if (
           Object.prototype.hasOwnProperty.call(guidata[objName], 'visibility')
         ) {
-          const obj = this._meshGroup?.getObjectByName(objName);
           const explodedLineHelper =
             this._explodedViewLinesHelperGroup?.getObjectByName(objName);
           const objGuiData = guidata[objName];
 
-          if (obj && objGuiData) {
+          if (objGuiData) {
             obj.visible = objGuiData['visibility'];
 
             if (explodedLineHelper) {
@@ -948,6 +952,13 @@ export class MainView extends React.Component<IProps, IStates> {
             }
           }
         }
+        if ('color' in guidata[objName]) {
+          const rgba = guidata[objName]['color'] as number[];
+          const color = new THREE.Color(rgba[0], rgba[1], rgba[2]);
+          obj.material.color = color;
+        } else {
+          obj.material.color = DEFAULT_MESH_COLOR;
+        }
       }
     }
   }
diff --git a/yarn.lock b/yarn.lock
index 0b0166b8..85d294d7 100644
--- a/yarn.lock
+++ b/yarn.lock
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