DeepLabCut · MMathisLab · Jun 27, 2026 · Jun 23, 2026 · Jun 23, 2026 · Jun 23, 2026
diff --git a/deeplabcut/gui/tabs/create_videos.py b/deeplabcut/gui/tabs/create_videos.py
@@ -27,6 +27,8 @@ class CreateVideos(DefaultTab):
     def __init__(self, root, parent, h1_description):
         super().__init__(root, parent, h1_description)
 
+        self.skeleton_builder = None
+
         self.bodyparts_to_use = self.root.all_bodyparts
         self._set_page()
 
@@ -71,6 +73,9 @@ def _set_page(self):
         self.help_button.clicked.connect(self.show_help_dialog)
         self.main_layout.addWidget(self.help_button, alignment=Qt.AlignLeft)
 
+    def _on_skeleton_builder_destroyed(self):
+        self.skeleton_builder = None
+
     def show_help_dialog(self):
         dialog = QtWidgets.QDialog(self)
         layout = QtWidgets.QVBoxLayout()
@@ -287,4 +292,10 @@ def create_videos(self):
     def build_skeleton(self, *args):
         from deeplabcut.gui.widgets import SkeletonBuilder
 
-        SkeletonBuilder(self.root.config)
+        if self.skeleton_builder is None:
+            self.skeleton_builder = SkeletonBuilder(
+                config_path=self.root.config,
+                parent=self.root,
+            )
+            self.skeleton_builder.destroyed.connect(self._on_skeleton_builder_destroyed)
+            self.skeleton_builder.show()
diff --git a/deeplabcut/gui/tabs/label_frames.py b/deeplabcut/gui/tabs/label_frames.py
@@ -18,8 +18,7 @@
 
 from deeplabcut.generate_training_dataset import check_labels
 from deeplabcut.gui.components import DefaultTab
-from deeplabcut.gui.widgets import launch_napari
-from deeplabcut.utils.skeleton import SkeletonBuilder
+from deeplabcut.gui.widgets import SkeletonBuilder, launch_napari
 
 
 def label_frames(config_path: str | Path | None = None, image_folder: str | None = None):
@@ -103,6 +102,7 @@ def __init__(self, root, parent, h1_description):
         super().__init__(root, parent, h1_description)
 
         self._set_page()
+        self.skeleton_builder = None
 
     def _set_page(self):
         self.label_frames_btn = QtWidgets.QPushButton("Label Frames")
@@ -139,5 +139,14 @@ def check_labels(self):
         labeled_images = (Path(self.root.config).parent / "labeled-data").rglob("*_labeled/*.png")
         _ = launch_napari(labeled_images, plugin="napari", stack=True)
 
+    def _on_skeleton_builder_destroyed(self):
+        self.skeleton_builder = None
+
     def build_skeleton(self, *args):
-        SkeletonBuilder(self.root.config)
+        if self.skeleton_builder is None:
+            self.skeleton_builder = SkeletonBuilder(
+                config_path=self.root.config,
+                parent=self.root,
+            )
+            self.skeleton_builder.show()
+            self.skeleton_builder.destroyed.connect(self._on_skeleton_builder_destroyed)
diff --git a/deeplabcut/gui/widgets.py b/deeplabcut/gui/widgets.py
@@ -19,7 +19,7 @@
 from matplotlib.figure import Figure
 from matplotlib.widgets import Button, LassoSelector, RectangleSelector
 from PySide6 import QtCore, QtWidgets
-from PySide6.QtGui import QAction, QCursor, QStandardItem, QStandardItemModel
+from PySide6.QtGui import QAction, QCursor, QStandardItem, QStandardItemModel, Qt
 
 from deeplabcut.utils import auxiliaryfunctions
 from deeplabcut.utils.auxfun_videos import VideoWriter
@@ -522,30 +522,32 @@ def display_help(self, *args):
         )
 
 
-class SkeletonBuilder(QtWidgets.QDialog, BaseSkeletonBuilder):
-    def __init__(self, config_path, parent=None):
+class SkeletonBuilder(BaseSkeletonBuilder, QtWidgets.QDialog):
+    def __init__(self, config_path, *, parent=None):
         QtWidgets.QDialog.__init__(self, parent)
         self._parent = parent
         self.setWindowTitle("Skeleton Builder")
+        self.setAttribute(Qt.WA_DeleteOnClose, True)
         BaseSkeletonBuilder.__init__(self, config_path)
 
     def build_ui(self):
         self.fig = Figure()
-        self.ax = self.fig.add_subplot(111)
-        self.ax.axis("off")
+        self.canvas = FigureCanvas(self.fig)
+
+        self._ax = self.fig.add_subplot(111)
+        self._ax.axis("off")
 
-        ax_clear = self.fig.add_axes([0.85, 0.55, 0.1, 0.1])
-        ax_export = self.fig.add_axes([0.85, 0.45, 0.1, 0.1])
+        ax_clear = self.fig.add_axes(self.clear_button_axes)
+        ax_export = self.fig.add_axes(self.export_button_axes)
 
-        self.clear_button = Button(ax_clear, "Clear")
+        self.clear_button = Button(ax_clear, self.clear_button_text)
         self.clear_button.on_clicked(self.clear)
 
-        self.export_button = Button(ax_export, "Export")
+        self.export_button = Button(ax_export, self.export_button_text)
         self.export_button.on_clicked(self.export)
 
         self.fig.canvas.mpl_connect("pick_event", self.on_pick)
 
-        self.canvas = FigureCanvas(self.fig)
         layout = QtWidgets.QVBoxLayout(self)
         layout.addWidget(self.canvas)
         self.setLayout(layout)
@@ -554,18 +556,17 @@ def build_ui(self):
         hi = np.nanmax(self.xy, axis=0)
         center = (hi + lo) / 2
         w, h = hi - lo
-        ampl = 1.3
-        w *= ampl
-        h *= ampl
-
-        self.ax.set_xlim(center[0] - w / 2, center[0] + w / 2)
-        self.ax.set_ylim(center[1] - h / 2, center[1] + h / 2)
-        self.ax.imshow(self.image)
-        self.ax.scatter(*self.xy.T, s=self.cfg["dotsize"] ** 2)
-        self.ax.add_collection(self.lines)
-        self.ax.invert_yaxis()
-
-        self.lasso = LassoSelector(self.ax, onselect=self.on_select)
+        w *= self.ampl
+        h *= self.ampl
+
+        self._ax.set_xlim(center[0] - w / 2, center[0] + w / 2)
+        self._ax.set_ylim(center[1] - h / 2, center[1] + h / 2)
+        self._ax.imshow(self.image)
+        self._ax.scatter(*self.xy.T, s=self.cfg["dotsize"] ** 2)
+        self._ax.add_collection(self.lines)
+        self._ax.invert_yaxis()
+
+        self.lasso = LassoSelector(self._ax, onselect=self.on_select)
         self.canvas.draw_idle()
 
     def read_config(self, config_path):
@@ -581,3 +582,12 @@ def write_config(self, config_path, cfg):
     def display(self):
         # No-op, the dialog is shown/exec'd by the caller
         pass
+
+    def export(self, *args):
+        success = super().export(*args)
+        if success:
+            self._parent.logger.info("Skeleton exported successfully.")
+            self._parent.status_bar.showMessage("Skeleton exported successfully.", 5000)
+        else:
+            self._parent.logger.warning("Failed to export skeleton.")
+            self._parent.status_bar.showMessage("Failed to export skeleton.", 5000)
diff --git a/deeplabcut/utils/skeleton.py b/deeplabcut/utils/skeleton.py
@@ -18,6 +18,7 @@
 Licensed under GNU Lesser General Public License v3.0
 """
 
+import logging
 import os
 import warnings
 
@@ -33,12 +34,23 @@
 from deeplabcut.core.config import read_config_as_dict, write_config
 from deeplabcut.generate_training_dataset.trainingsetmanipulation import drop_likelihood_columns
 
+logger = logging.getLogger(__name__)
+
 
 class SkeletonBuilder:
+    ### Usage parameters
+    lasso_select_size = 10
+    clear_button_axes = [0.85, 0.55, 0.1, 0.1]
+    clear_button_text = "Clear"
+    export_button_axes = [0.85, 0.45, 0.1, 0.1]
+    export_button_text = "Save"
+    ampl = 1.3  # Amplification factor for the zoomed-in view of the animal
+
     def __init__(self, config_path):
         self.config_path = config_path
         self.cfg = read_config_as_dict(config_path)
         # Find uncropped labeled data
+        self._ax = None
         self.df = None
         found = False
         root = os.path.join(self.cfg["project_path"], "labeled-data")
@@ -74,8 +86,9 @@ def __init__(self, config_path):
         self.inds = set()
         self.segs = set()
         # Draw the skeleton if already existent
-        if self.cfg["skeleton"]:
-            for bone in self.cfg["skeleton"]:
+        skeleton = self.cfg.get("skeleton", [])
+        if skeleton:
+            for bone in skeleton:
                 pair = np.flatnonzero(self.bpts.isin(bone))
                 if len(pair) != 2:
                     continue
@@ -89,28 +102,27 @@ def __init__(self, config_path):
 
     def build_ui(self):
         self.fig = plt.figure()
-        ax = self.fig.add_subplot(111)
-        ax.axis("off")
+        self._ax = self.fig.add_subplot(111)
+        self._ax.axis("off")
         lo = np.nanmin(self.xy, axis=0)
         hi = np.nanmax(self.xy, axis=0)
         center = (hi + lo) / 2
         w, h = hi - lo
-        ampl = 1.3
-        w *= ampl
-        h *= ampl
-        ax.set_xlim(center[0] - w / 2, center[0] + w / 2)
-        ax.set_ylim(center[1] - h / 2, center[1] + h / 2)
-        ax.imshow(self.image)
-        ax.scatter(*self.xy.T, s=self.cfg["dotsize"] ** 2)
-        ax.add_collection(self.lines)
-        ax.invert_yaxis()
-
-        self.lasso = LassoSelector(ax, onselect=self.on_select)
-        ax_clear = self.fig.add_axes([0.85, 0.55, 0.1, 0.1])
-        ax_export = self.fig.add_axes([0.85, 0.45, 0.1, 0.1])
-        self.clear_button = Button(ax_clear, "Clear")
+        w *= self.ampl
+        h *= self.ampl
+        self._ax.set_xlim(center[0] - w / 2, center[0] + w / 2)
+        self._ax.set_ylim(center[1] - h / 2, center[1] + h / 2)
+        self._ax.imshow(self.image)
+        self._ax.scatter(*self.xy.T, s=self.cfg["dotsize"] ** 2)
+        self._ax.add_collection(self.lines)
+        self._ax.invert_yaxis()
+
+        self.lasso = LassoSelector(self._ax, onselect=self.on_select)
+        ax_clear = self.fig.add_axes(self.clear_button_axes)
+        ax_export = self.fig.add_axes(self.export_button_axes)
+        self.clear_button = Button(ax_clear, self.clear_button_text)
         self.clear_button.on_clicked(self.clear)
-        self.export_button = Button(ax_export, "Export")
+        self.export_button = Button(ax_export, self.export_button_text)
         self.export_button.on_clicked(self.export)
         self.fig.canvas.mpl_connect("pick_event", self.on_pick)
 
@@ -145,17 +157,53 @@ def read_config(self, config_path):
     def write_config(self, config_path, cfg):
         write_config(config_path, cfg)
 
-    def export(self, *args):
-        inds_flat = set(ind for pair in self.inds for ind in pair)
-        unconnected = [i for i in range(len(self.xy)) if i not in inds_flat]
-        if len(unconnected):
-            warnings.warn(
-                "You didn't connect all the bodyparts (which is fine!). This is just a note to let you know.",
-                stacklevel=2,
-            )
-        # sort to ensure consistent order in config.yaml
-        self.cfg["skeleton"] = [tuple(self.bpts[list(pair)]) for pair in sorted(self.inds)]
-        self.write_config(self.config_path, self.cfg)
+    def _show_export_feedback(self):
+        if not hasattr(self, "export_button"):
+            return
+
+        button = self.export_button
+        canvas = self.fig.canvas
+
+        original_text = button.label.get_text()
+        original_color = button.ax.get_facecolor()
+
+        n_edges = len(self.cfg.get("skeleton") or [])
+        button.label.set_text(f"Saved {n_edges}")
+        button.ax.set_facecolor("#c8e6c9")  # light green
+        canvas.draw_idle()
+
+        def reset_button():
+            button.label.set_text(original_text)
+            button.ax.set_facecolor(original_color)
+            canvas.draw_idle()
+            return False  # stop Matplotlib timer
+
+        timer = canvas.new_timer(interval=1200)
+        timer.add_callback(reset_button)
+
+        # Keep a reference so the timer is not garbage-collected.
+        self._export_feedback_timer = timer
+        timer.start()
+
+    def export(self, *args) -> bool:
+        try:
+            inds_flat = set(ind for pair in self.inds for ind in pair)
+            unconnected = [i for i in range(len(self.xy)) if i not in inds_flat]
+            # if empty, mention we are saving an empty skeleton
+            if not self.inds:
+                logger.warning("No bodyparts are connected. Saving an empty skeleton.")
+            elif len(unconnected):
+                logger.warning(
+                    "Not all bodyparts are connected. Note that connecting all bodyparts is not necessary.",
+                )
+            # sort to ensure consistent order in config.yaml
+            self.cfg["skeleton"] = [tuple(self.bpts[list(pair)]) for pair in sorted(self.inds)]
+            self.write_config(self.config_path, self.cfg)
+            self._show_export_feedback()
+            return True
+        except Exception as e:
+            logger.warning(f"Failed to export skeleton: {e}", stacklevel=2)
+            return False
 
     def on_pick(self, event):
         if event.mouseevent.button == 3:
@@ -169,16 +217,27 @@ def on_pick(self, event):
             self.fig.canvas.draw_idle()
 
     def on_select(self, verts):
-        # self.path = Path(verts)
-        # self.verts = verts
-        inds = self.tree.query_ball_point(verts, 5)
+        # Transform keypoints and lasso vertices from image/data coordinates
+        # into display coordinates. This makes the grab radius independent of
+        # the image resolution and current zoom level.
+        xy_display = self._ax.transData.transform(self.xy)
+        verts_display = self._ax.transData.transform(np.asarray(verts))
+
+        tree_display = KDTree(xy_display)
+        inds = tree_display.query_ball_point(
+            verts_display,
+            self.lasso_select_size,
+        )
+
         inds_unique = []
         for lst in inds:
             if len(lst) and lst[0] not in inds_unique:
                 inds_unique.append(lst[0])
+
         for pair in zip(inds_unique, inds_unique[1:], strict=False):
             pair_sorted = tuple(sorted(pair))
             self.inds.add(pair_sorted)
             self.segs.add(tuple(map(tuple, self.xy[pair_sorted, :])))
-        self.lines.set_segments(self.segs)
+
+        self.lines.set_segments(list(self.segs))
         self.fig.canvas.draw_idle()
diff --git a/tests/utils/test_skeleton.py b/tests/utils/test_skeleton.py
@@ -41,6 +41,9 @@ def make_test_builder():
 
 def attach_fake_canvas(builder):
     builder.fig = Figure()
+    builder._ax = builder.fig.add_subplot(111)
+    builder._ax.set_xlim(-5, 25)
+    builder._ax.set_ylim(-5, 5)
     builder.fig.canvas.draw_idle = lambda: None
 
 
@@ -136,7 +139,7 @@ def test_clear_resets_indices_segments_and_linecollection():
 # ---------------------------------------------------------------------
 
 
-def test_export_sorts_pairs_and_warns_for_unconnected(monkeypatch):
+def test_export_sorts_pairs_and_warns_for_unconnected(monkeypatch, caplog):
     builder = make_test_builder()
     builder.config_path = "dummy_config.yaml"
     builder.xy = np.array(
@@ -159,8 +162,9 @@ def fake_write_config(path, cfg):
 
     monkeypatch.setattr(skeleton_mod, "write_config", fake_write_config)
 
-    with pytest.warns(UserWarning, match="didn't connect all the bodyparts"):
+    with caplog.at_level("INFO"):
         builder.export()
+    assert "Not all bodyparts are connected" in caplog.text
 
     assert captured["path"] == "dummy_config.yaml"
     assert captured["cfg"]["skeleton"] == [