🆕 Address TIAViz Review Comments

tiatoolbox/annotation/storage.py

@@ -1990,6 +1990,20 @@ def transform_geometry(geom: Geometry) -> Geometry:
             )
             for feature in geojson["features"]
         ]
+        # check for presence of 'nucleusGeometry' key in features
+        # if present, add them (qupath export format)
+        annotations += [
+            transform(
+                Annotation(
+                    transform_geometry(
+                        feature2geometry(feature["nucleusGeometry"]),
+                    ),
+                    {},
+                ),
+            )
+            for feature in geojson["features"]
+            if "nucleusGeometry" in feature
+        ]
 
         logger.info("Adding %d annotations.", len(annotations))
         self.append_many(annotations)

tiatoolbox/utils/visualization.py

@@ -850,11 +850,41 @@ def render_pt(
                 top_left,
                 scale,
             )[0][0],
-            np.maximum(self.edge_thickness, 1),
+            np.maximum(int(16 / scale**0.5), 1),
             col,
-            thickness=self.thickness,
+            thickness=-1,
         )
 
+    def render_pts(
+        self: AnnotationRenderer,
+        tile: np.ndarray,
+        annotation: Annotation,
+        top_left: tuple[float, float],
+        scale: float,
+    ) -> None:
+        """Render a multipoint annotation onto a tile using cv2.
+
+        Args:
+            tile (ndarray):
+                The rgb(a) tile image to render onto.
+            annotation (Annotation):
+                The annotation to render.
+            top_left (tuple):
+                The top left corner of the tile in wsi.
+            scale (float):
+                The zoom scale at which we are rendering.
+
+        """
+        col = self.get_color(annotation, edge=False)
+        for pt in annotation.coords:
+            cv2.circle(
+                tile,
+                self.to_tile_coords([pt], top_left, scale)[0][0],
+                np.maximum(int(16 / scale**0.5), 1),
+                col,
+                thickness=-1,
+            )
+
     def render_line(
         self: AnnotationRenderer,
         tile: np.ndarray,
@@ -1057,5 +1087,7 @@ def render_by_type(
             self.render_poly(tile, annotation, top_left, scale)
         elif geom_type == GeometryType.LINE_STRING:
             self.render_line(tile, annotation, top_left, scale)
+        elif geom_type == GeometryType.MULTI_POINT:
+            self.render_pts(tile, annotation, top_left, scale)
         else:
             logger.warning("Unknown geometry: %s", geom_type, stacklevel=3)

tiatoolbox/visualization/bokeh_app/main.py

@@ -512,7 +512,6 @@ def add_layer(lname: str) -> None:
             end=1,
             value=0.75,
             step=0.01,
-            title=lname,
             height=40,
             width=100,
             max_width=90,
@@ -1054,7 +1053,9 @@ def layer_slider_cb(
             UI["vstate"].layer_dict[obj.name.split("_")[0]]
         ].glyph.line_alpha = new
     else:
-        UI["p"].renderers[UI["vstate"].layer_dict[obj.name.split("_")[0]]].alpha = new
+        UI["p"].renderers[
+            UI["vstate"].layer_dict["_".join(obj.name.split("_")[0:-1])]
+        ].alpha = new
 
 
 def color_input_cb(

tiatoolbox/visualization/tileserver.py

@@ -511,7 +511,7 @@ def change_overlay(self: TileServer) -> str:
         overlay_path = self.decode_safe_name(overlay_path)
 
         if overlay_path.suffix in [".jpg", ".png", ".tiff", ".svs", ".ndpi", ".mrxs"]:
-            layer = f"layer{len(self.pyramids[session_id])}"
+            layer = overlay_path.stem
             if overlay_path.suffix == ".tiff":
                 self.layers[session_id][layer] = OpenSlideWSIReader(
                     overlay_path,