Add low-res sample data

Author: constantinpape

flamingo_tools/model_utils.py

@@ -53,6 +53,7 @@ def get_device(device: Optional[Union[str, torch.device]] = None) -> Union[str,
     return device
 
 
+# FIXME: SGN-lowres seems to be the wrong model and doesn't work well on the sample data.
 def get_model_registry() -> None:
     """Get the model registry for downloading pre-trained CochleaNet models.
     """

flamingo_tools/napari.yaml

@@ -13,6 +13,7 @@ contributions:
     - id: cochlea_net.detect
       python_name: flamingo_tools.plugin.detection_widget:DetectionWidget
       title: Detection
+
     # Add a measurement widget?
     # Add a labeling / classification widget?
 
@@ -26,6 +27,12 @@ contributions:
     - id: cochlea_net.sample_data_ctbp2
       python_name: flamingo_tools.test_data:sample_data_ctbp2
       title: Example CtBP2 data
+    - id: cochlea_net.sample_data_pv_lowres
+      python_name: flamingo_tools.test_data:sample_data_pv_lowres
+      title: Example PV lowres data
+    - id: cochlea_net.sample_data_myo_lowres
+      python_name: flamingo_tools.test_data:sample_data_myo_lowres
+      title: Example MYO lowres data
 
   widgets:
     - command: cochlea_net.segment
@@ -43,3 +50,9 @@ contributions:
     - command: cochlea_net.sample_data_ctbp2
       display_name: Sample Data CtBP2
       key: cochlea-net-ctbp2
+    - command: cochlea_net.sample_data_pv_lowres
+      display_name: Sample Data PV Lowres
+      key: cochlea-net-pv-lowres
+    - command: cochlea_net.sample_data_myo_lowres
+      display_name: Sample Data MYO Lowres
+      key: cochlea-net-myo-lowres

flamingo_tools/plugin/segmentation_widget.py

@@ -65,7 +65,7 @@ def load_model_widget(self):
         model_list = list(get_model_registry().urls.keys())
 
         # Exclude the detection models.
-        segmentation_models = ["SGN", "IHC"]
+        segmentation_models = ["SGN", "IHC", "SGN-lowres", "IHC-lowres"]
         model_list = [name for name in model_list if name in segmentation_models]
 
         models = ["- choose -"] + model_list

flamingo_tools/test_data.py

@@ -100,15 +100,15 @@ def _sample_registry():
         "PV": "https://owncloud.gwdg.de/index.php/s/JVZCOpkILT70sdv/download",
         "VGlut3": "https://owncloud.gwdg.de/index.php/s/LvGXh0xQR9IKvNk/download",
         "CTBP2": "https://owncloud.gwdg.de/index.php/s/qaffCaF1sGpqlT3/download",
-        "PV-lowres": "",
-        "IHC-lowres": "",
+        "PV-lowres": "https://owncloud.gwdg.de/index.php/s/9BjuMIo9ulrqKVp/download",
+        "MYO-lowres": "https://owncloud.gwdg.de/index.php/s/aKJrQs1zkBtFBI9/download",
     }
     registry = {
         "PV": "fbf50cc9119f2dd2bd4dac7d76b746b7d42cab33b94b21f8df304478dd51e632",
         "VGlut3": "6a3af6ffce3d06588ffdc73df356ac64b83b53aaf6aabeabd49ef6d11d927e20",
         "CTBP2": "8dcd5f1ebb35194f328788594e275f2452de0e28c85073578dac7100d83c45fc",
-        "PV-lowres": "",
-        "IHC-lowres": "",
+        "PV-lowres": "325684d5a74eed356ac7e0d7720a727a58862f6d26c2884937eae7013f51bdc9",
+        "MYO-lowres": "386f0b66a1716268b6e80d694e0a5170fd06f5b6f7ad1698ea4a0bb0464a4a5c",
     }
     cache_dir = get_cache_dir()
     data_registry = pooch.create(
@@ -148,8 +148,8 @@ def sample_data_pv_lowres():
     return [(data, add_image_kwargs)]
 
 
-def sample_data_ihc_lowres():
-    data_path = _sample_registry().fetch("IHC-lowres")
+def sample_data_myo_lowres():
+    data_path = _sample_registry().fetch("MYO-lowres")
     data = imageio.imread(data_path, extension=".tif")
-    add_image_kwargs = {"name": "IHC-lowres", "colormap": "gray"}
+    add_image_kwargs = {"name": "MYO-lowres", "colormap": "gray"}
     return [(data, add_image_kwargs)]