diff --git a/sloth/annotations/container.py b/sloth/annotations/container.py
index f531c70..e832704 100644
--- a/sloth/annotations/container.py
+++ b/sloth/annotations/container.py
@@ -77,8 +77,8 @@ class AnnotationContainer:
         """
         if not filename:
             raise InvalidArgumentException("filename cannot be empty")
-        self.annotations_ = self.parseFromFile(filename)
         self.filename_ = filename
+        return self.parseFromFile(filename)
 
     def parseFromFile(self, filename):
         """
@@ -96,10 +96,10 @@ class AnnotationContainer:
         """
         if not filename:
             filename = self.filename()
-        self.serializeToFile(filename)
+        self.serializeToFile(filename, annotations)
         self.filename_ = filename
 
-    def serializeToFile(self, filename):
+    def serializeToFile(self, filename, annotations):
         """
         Serialize the annotations to disk. Must be implemented in the subclass.
         """
@@ -109,18 +109,6 @@ class AnnotationContainer:
             "AnnotationContainer.save()"
         )
 
-    def setAnnotations(self, annotations):
-        """
-        Set the current annotations. Expects a list of python dictionaries.
-        """
-        self.annotations_ = annotations
-
-    def annotations(self):
-        """
-        Returns the current annotations as list of python dictionaries.
-        """
-        return self.annotations_
-
     def _fullpath(self, filename):
         """
         Calculate the fullpath to the file, assuming that
@@ -152,22 +140,6 @@ class AnnotationContainer:
         fullpath = self._fullpath(filename)
         #TODO load video
 
-    def numFiles(self):
-        return len(self.annotations())
-
-    def numAnnotations(self):
-        if self.annotations() is None:
-            return 0
-        num = 0
-        for file in self.annotations():
-            if file['type'] == 'image':
-                num += len(file['annotations'])
-            elif file['type'] == 'video':
-                for frame in file['frames']:
-                    num += len(frame['annotations'])
-        return num
-
-
 class PickleContainer(AnnotationContainer):
     """
     Simple container which pickles the annotations to disk.
@@ -180,13 +152,13 @@ class PickleContainer(AnnotationContainer):
         f = open(fname, "rb")
         return pickle.load(f)
 
-    def serializeToFile(self, fname):
+    def serializeToFile(self, fname, annotations):
         """
         Overwritten to write pickle files.
         """
         # TODO make all image filenames relative to the label file
         f = open(fname, "wb")
-        pickle.dump(self.annotations(), f)
+        pickle.dump(annotations, f)
 
 
 class JsonContainer(AnnotationContainer):
@@ -201,13 +173,13 @@ class JsonContainer(AnnotationContainer):
         f = open(fname, "r")
         return json.load(f)
 
-    def serializeToFile(self, fname):
+    def serializeToFile(self, fname, annotations):
         """
         Overwritten to write JSON files.
         """
         # TODO make all image filenames relative to the label file
         f = open(fname, "w")
-        json.dump(self.annotations(), f, indent=4)
+        json.dump(annotations, f, indent=4)
 
 
 class YamlContainer(AnnotationContainer):
@@ -222,13 +194,13 @@ class YamlContainer(AnnotationContainer):
         f = open(fname, "r")
         return yaml.load(f)
 
-    def serializeToFile(self, fname):
+    def serializeToFile(self, fname, annotations):
         """
         Overwritten to write YAML files.
         """
         # TODO make all image filenames relative to the label file
         f = open(fname, "w")
-        yaml.dump(self.annotations(), f)
+        yaml.dump(annotations, f)
 
 
 class FileNameListContainer(AnnotationContainer):
@@ -253,7 +225,7 @@ class FileNameListContainer(AnnotationContainer):
 
         return annotations
 
-    def serializeToFile(self, filename):
+    def serializeToFile(self, filename, annotations):
         raise NotImplemented("FileNameListContainer.save() is not implemented yet.")
 
 class FeretContainer(AnnotationContainer):
@@ -286,7 +258,7 @@ class FeretContainer(AnnotationContainer):
 
         return annotations
 
-    def serializeToFile(self, filename):
+    def serializeToFile(self, filename, annotations):
         """
         Not implemented yet.
         """
diff --git a/sloth/annotations/model.py b/sloth/annotations/model.py
index e5bc429..1980499 100644
--- a/sloth/annotations/model.py
+++ b/sloth/annotations/model.py
@@ -169,6 +169,13 @@ class RootModelItem(ModelItem):
         items = [FileModelItem.create(fi) for fi in fileinfos]
         self.appendChildren(items)
 
+    def numFiles(self):
+        return len(self.children())
+
+    def numAnnotations(self):
+        # TODO
+        return 0
+
 class FileModelItem(ModelItem):
     def __init__(self, fileinfo):
         ModelItem.__init__(self)
@@ -387,6 +394,9 @@ class AnnotationModel(QAbstractItemModel):
         return QVariant()
 
     # Own methods
+    def root(self):
+        return self._root
+
     def dirty(self):
         return self._dirty
 
diff --git a/sloth/core/labeltool.py b/sloth/core/labeltool.py
index bcdfe84..7f594af 100755
--- a/sloth/core/labeltool.py
+++ b/sloth/core/labeltool.py
@@ -201,9 +201,9 @@ class LabelTool(QObject):
         try:
             self.container_ = self.container_factory_.create(fname)
             self.container_.load(fname)
+            self._model = AnnotationModel(self.container_.load(fname))
             msg = "Successfully loaded %s (%d files, %d annotations)" % \
-                    (fname, self.container_.numFiles(), self.container_.numAnnotations())
-            self._model = AnnotationModel(self.container_.annotations())
+                    (fname, self._model.root().numFiles(), self._model.root().numAnnotations())
         except Exception, e:
             msg = "Error: Loading failed (%s)" % str(e)
 
@@ -220,10 +220,13 @@ class LabelTool(QObject):
                 newcontainer.setAnnotations(self.container_.annotations())
                 self.container_ = newcontainer
 
-            self.container_.save(fname)
+            # Get annotations dict
+            ann = self._model.getAnnotations()
+
+            self.container_.save(fname, ann)
             #self._model.writeback() # write back changes that are cached in the model itself, e.g. mask updates
             msg = "Successfully saved %s (%d files, %d annotations)" % \
-                    (fname, self.container_.numFiles(), self.container_.numAnnotations())
+                    (fname, self._model.root().numFiles(), self._model.root().numAnnotations())
             success = True
             self._model.setDirty(False)
         except Exception as e: