Add neurons and labels sample data

pyproject.toml

@@ -29,20 +29,20 @@ requires-python = ">=3.10"
 # or any other Qt bindings directly (e.g. PyQt5, PySide2).
 # See best practices: https://napari.org/stable/plugins/building_a_plugin/best_practices.html
 dependencies = [
-    "bioio",
-    "bioio-imageio",
-    "bioio-ome-tiff",
+    "pooch",
+    "ndevio>=0.5.2",
+    # "bioio",
+    # "bioio-imageio",
+    # "bioio-ome-tiff",
 ]
 
-[project.optional-dependencies]
-# Allow easily installation with the full, default napari installation
-# (including Qt backend) using ndev-sampledata[all].
-all = ["napari[all]"]
-testing = [
-    "napari",
-    "tox",
-    "pytest",  # https://docs.pytest.org/en/latest/contents.html
-    "pytest-cov",  # https://pytest-cov.readthedocs.io/en/latest/
+[dependency-groups]
+dev = [
+    "tox-uv",
+    "pytest",
+    "pytest-cov",
+    "pre-commit",
+    "napari[pyqt6]",
 ]
 
 [project.entry-points."napari.manifest"]

src/ndev_sampledata/_sample_data.py

@@ -12,7 +12,11 @@
 from pathlib import Path
 from typing import TYPE_CHECKING
 
+import pooch
 from bioio import BioImage
+from bioio_imageio import Reader as ImageIOReader
+from bioio_ome_tiff import Reader as OmeTiffReader
+from ndevio._napari_reader import napari_reader_function
 
 if TYPE_CHECKING:
     from napari.types import LayerDataTuple
@@ -21,7 +25,7 @@
 
 
 def ndev_logo() -> list[LayerDataTuple]:
-    img = BioImage(sample_dir / "ndev-logo.png")
+    img = BioImage(sample_dir / "ndev-logo.png", reader=ImageIOReader)
     data = img.data.squeeze()
     metadata = {
         "name": "ndev logo",
@@ -32,7 +36,10 @@ def ndev_logo() -> list[LayerDataTuple]:
 
 
 def neuron_2d_4ch() -> list[LayerDataTuple]:
-    img = BioImage(sample_dir / "neuron-4Ch.tiff")
+    img = BioImage(
+        sample_dir / "neuron-4Ch-crop.tiff",
+        reader=OmeTiffReader,
+    )
     scale = (img.physical_pixel_sizes.Y, img.physical_pixel_sizes.X)
     ch0 = (
         img.get_image_data("YX", C=0),
@@ -74,7 +81,10 @@ def neuron_2d_4ch() -> list[LayerDataTuple]:
 
 
 def scratch_assay() -> list[LayerDataTuple]:
-    img = BioImage(sample_dir / "scratch-assay-labeled-10T-2Ch.tiff")
+    img = BioImage(
+        sample_dir / "scratch-assay-labeled-10T-2Ch.tiff",
+        reader=OmeTiffReader,
+    )
     scale = (img.physical_pixel_sizes.Y, img.physical_pixel_sizes.X)
     ch0 = (
         img.get_image_data("TYX", C=0),
@@ -121,7 +131,10 @@ def scratch_assay() -> list[LayerDataTuple]:
 
 
 def neocortex() -> list[LayerDataTuple]:
-    img = BioImage(sample_dir / "neocortex-3Ch.tiff")
+    img = BioImage(
+        sample_dir / "neocortex-3Ch-crop.tiff",
+        reader=OmeTiffReader,
+    )
     scale = (img.physical_pixel_sizes.Y, img.physical_pixel_sizes.X)
     ch0 = (
         img.get_image_data("YX", C=0),
@@ -151,3 +164,38 @@ def neocortex() -> list[LayerDataTuple]:
         },
     )
     return [ch0, ch1, ch2]
+
+
+def neuron_raw() -> list[LayerDataTuple]:
+    # use pooch to get the download from remote URL if not present locally
+    neuron_raw_path = pooch.retrieve(
+        url="doi:10.5281/zenodo.17836129/neuron-4Ch_raw.tiff",
+        known_hash="md5:5d3e42bca2085e8588b6f23cf89ba87c",
+        fname="neuron-4Ch_raw.tiff",
+        path=sample_dir,
+    )
+
+    return napari_reader_function(
+        path=neuron_raw_path,
+        reader=OmeTiffReader,
+        in_memory=True,
+        layer_type="image",
+    )
+
+
+def neuron_labels() -> list[LayerDataTuple]:
+    return napari_reader_function(
+        path=sample_dir / "neuron-4Ch_labels.tiff",
+        reader=OmeTiffReader,
+        in_memory=True,
+        layer_type="labels",
+    )
+
+
+def neuron_labels_processed() -> list[LayerDataTuple]:
+    return napari_reader_function(
+        path=sample_dir / "neuron-4Ch_labels_processed.tiff",
+        reader=OmeTiffReader,
+        in_memory=True,
+        layer_type="labels",
+    )

src/ndev_sampledata/napari.yaml

@@ -18,16 +18,34 @@ contributions:
     - id : ndev-sampledata.make_neocortex
       python_name: ndev_sampledata._sample_data:neocortex
       title: Load neocortex data
+    - id: ndev-sampledata.make_neuron_raw
+      python_name: ndev_sampledata._sample_data:neuron_raw
+      title: Load raw neuron data
+    - id: ndev-sampledata.make_neuron_labels
+      python_name: ndev_sampledata._sample_data:neuron_labels
+      title: Load neuron labels data
+    - id: ndev-sampledata.make_neuron_labels_processed
+      python_name: ndev_sampledata._sample_data:neuron_labels_processed
+      title: Load processed neuron labels data
   sample_data:
     - command: ndev-sampledata.make_ndev_logo
       display_name: ndev logo
       key: unique_id.0
     - command: ndev-sampledata.make_neuron_2d_4ch
-      display_name: Neuron (2D+4Ch)
+      display_name: Neuron Cropped (2D+4Ch)
       key: unique_id.1
     - command: ndev-sampledata.make_scratch_assay
       display_name: Scratch Assay Labeled (10T+2Ch)
       key: unique_id.2
     - command: ndev-sampledata.make_neocortex
       display_name: Neocortex (3Ch)
       key: unique_id.3
+    - command: ndev-sampledata.make_neuron_raw
+      display_name: Neuron Raw (2D+4Ch) (32MB)
+      key: unique_id.4
+    - command: ndev-sampledata.make_neuron_labels
+      display_name: Neuron Labels (2D+4Ch)
+      key: unique_id.5
+    - command: ndev-sampledata.make_neuron_labels_processed
+      display_name: Neuron Labels Processed (2D+4Ch)
+      key: unique_id.6