✨ Add on-the-fly Registered Slide Visualization

tiatoolbox/visualization/bokeh_app/main.py

@@ -714,8 +714,13 @@ def populate_layer_list(slide_name: str, overlay_path: Path) -> None:
         "*.jpg",
         "*.json",
         "*.tiff",
+        "*.mrxs",
+        "*.ndpi",
+        "*.svs",
+        "*.tif",
+        "*.npy",
+        "*.mha",
     ]:
-        file_list.extend(list(overlay_path.glob(str(Path("*") / ext))))
         file_list.extend(list(overlay_path.glob(ext)))
     file_list = [(str(p), str(p)) for p in sorted(file_list) if slide_name in str(p)]
     UI["layer_drop"].menu = file_list
@@ -726,7 +731,6 @@ def populate_slide_list(slide_folder: Path, search_txt: str | None = None) -> No
     file_list = []
     len_slidepath = len(slide_folder.parts)
     for ext in ["*.svs", "*ndpi", "*.tiff", "*.mrxs", "*.jpg", "*.png", "*.tif"]:
-        file_list.extend(list(Path(slide_folder).glob(str(Path("*") / ext))))
         file_list.extend(list(Path(slide_folder).glob(ext)))
     if search_txt is None:
         file_list = [
@@ -1003,7 +1007,8 @@ def layer_drop_cb(attr: MenuItemClick) -> None:
     if Path(attr.item).suffix in [".db", ".dat", ".geojson"]:
         update_ui_on_new_annotations(resp)
     else:
-        add_layer(resp)
+        if resp != "slide":
+            add_layer(resp)
         change_tiles(resp)
 
 

tiatoolbox/visualization/tileserver.py

@@ -25,7 +25,12 @@
 from tiatoolbox.tools.pyramid import AnnotationTileGenerator, ZoomifyGenerator
 from tiatoolbox.utils.misc import add_from_dat, store_from_dat
 from tiatoolbox.utils.visualization import AnnotationRenderer, colourise_image
-from tiatoolbox.wsicore.wsireader import OpenSlideWSIReader, VirtualWSIReader, WSIReader
+from tiatoolbox.wsicore.wsireader import (
+    OpenSlideWSIReader,
+    TransformedWSIReader,
+    VirtualWSIReader,
+    WSIReader,
+)
 
 if TYPE_CHECKING:  # pragma: no cover
     from matplotlib.colors import Colormap
@@ -510,6 +515,17 @@
         overlay_path = request.form["overlay_path"]
         overlay_path = self.decode_safe_name(overlay_path)
 
+        if overlay_path.suffix in [".npy", ".mha"]:
+            # loading a registration transformation
+            self.layers[session_id]["slide"] = TransformedWSIReader(
+                self.layers[session_id]["slide"].info.file_path,
+                transform=overlay_path,
+            )
+            self.pyramids[session_id]["slide"] = ZoomifyGenerator(
+                self.layers[session_id]["slide"],
+            )
+            return json.dumps("slide")
+
         if overlay_path.suffix in [".jpg", ".png", ".tiff", ".svs", ".ndpi", ".mrxs"]:
             layer = f"layer{len(self.pyramids[session_id])}"
             if overlay_path.suffix == ".tiff":