add ndevio-sampledata with new neuron labels

.gitignore

@@ -85,3 +85,8 @@ venv/
 # pixi environments
 .pixi/*
 !.pixi/config.toml
+
+# ndevio sampledata that is hosted on Zenodo
+src/ndevio/sampledata/data/neocortex-3Ch.tiff
+src/ndevio/sampledata/data/scratch-assay-labeled-10T-2Ch.tiff
+src/ndevio/sampledata/data/neuron-4Ch_raw.tiff

pyproject.toml

@@ -43,6 +43,7 @@ dependencies = [
     "bioio-imageio",
     "zarr>=3.1.3",  # tifffile's ZarrTiffStore needs set_partial_values/supports_partial_writes
     "napari-plugin-manager>=0.1.7",  # Renamed to PYPI from PIP for tool selection https://github.com/napari/napari-plugin-manager/pull/176
+    "pooch",  # for downloading sample data from remote URLs
 ]
 
 [project.optional-dependencies]
@@ -87,6 +88,9 @@ xfail_strict = true
 # filterwarnings = ["error"] # recommended by PP309
 log_cli_level = "INFO"
 testpaths = ["tests"]
+markers = [
+    "network: marks tests as requiring network access (deselect with '-m \"not network\"')",
+]
 
 [tool.coverage]
 report.fail_under = 80

src/ndevio/napari.yaml

@@ -3,7 +3,7 @@ display_name: ndevio
 # use 'hidden' to remove plugin from napari hub search results
 visibility: public
 # see https://napari.org/stable/plugins/technical_references/manifest.html#fields for valid categories
-# categories: []
+categories: ["IO", "Dataset", "Utilities"]
 contributions:
   commands:
     - id: ndevio.get_reader
@@ -15,6 +15,24 @@ contributions:
     - id: ndevio.make_utilities_widget
       python_name: ndevio.widgets:UtilitiesContainer
       title: I/O Utilities
+    - id: ndevio.make_ndev_logo
+      python_name: ndevio.sampledata:ndev_logo
+      title: Load ndev logo
+    - id: ndevio.make_scratch_assay
+      python_name: ndevio.sampledata:scratch_assay
+      title: Load scratch assay data
+    - id: ndevio.make_neocortex
+      python_name: ndevio.sampledata:neocortex
+      title: Load neocortex data
+    - id: ndevio.make_neuron_raw
+      python_name: ndevio.sampledata:neuron_raw
+      title: Load raw neuron data
+    - id: ndevio.make_neuron_labels
+      python_name: ndevio.sampledata:neuron_labels
+      title: Load neuron labels data
+    - id: ndevio.make_neuron_labels_processed
+      python_name: ndevio.sampledata:neuron_labels_processed
+      title: Load processed neuron labels data
   readers:
     - command: ndevio.get_reader
       accepts_directories: false
@@ -58,3 +76,22 @@ contributions:
       display_name: Install BioIO Reader Plugins
     - command: ndevio.make_utilities_widget
       display_name: I/O Utilities
+  sample_data:
+    - command: ndevio.make_ndev_logo
+      display_name: ndev logo
+      key: ndevio.ndev_logo
+    - command: ndevio.make_scratch_assay
+      display_name: Scratch Assay Labeled (10T+2Ch) (4MB)
+      key: ndevio.scratch_assay
+    - command: ndevio.make_neocortex
+      display_name: Neocortex (3Ch) (2MB)
+      key: ndevio.neocortex
+    - command: ndevio.make_neuron_raw
+      display_name: Neuron Raw (2D+4Ch) (32MB)
+      key: ndevio.neuron_raw
+    - command: ndevio.make_neuron_labels
+      display_name: Neuron Labels (2D+4Ch)
+      key: ndevio.neuron_labels
+    - command: ndevio.make_neuron_labels_processed
+      display_name: Neuron Labels Processed (2D+4Ch)
+      key: ndevio.neuron_labels_processed

src/ndevio/nimage.py

@@ -373,7 +373,9 @@ def _build_single_layer_tuple(
                 channel_idx, n_channels
             )
             meta["blending"] = (
-                "additive" if n_channels > 1 else "translucent_no_depth"
+                "additive"
+                if channel_idx > 0 and n_channels > 1
+                else "translucent_no_depth"
             )
 
         # Apply per-channel overrides

src/ndevio/sampledata/__init__.py

@@ -0,0 +1,19 @@
+"""Sample data for ndevio and the ndev-kit ecosystem."""
+
+from ndevio.sampledata._sample_data import (
+    ndev_logo,
+    neocortex,
+    neuron_labels,
+    neuron_labels_processed,
+    neuron_raw,
+    scratch_assay,
+)
+
+__all__ = [
+    "ndev_logo",
+    "neocortex",
+    "neuron_labels",
+    "neuron_labels_processed",
+    "neuron_raw",
+    "scratch_assay",
+]

src/ndevio/sampledata/_sample_data.py

@@ -0,0 +1,116 @@
+"""
+Sample data providers for napari.
+
+This module implements the "sample data" specification.
+see: https://napari.org/stable/plugins/building_a_plugin/guides.html#sample-data
+"""
+
+from __future__ import annotations
+
+from pathlib import Path
+from typing import TYPE_CHECKING
+
+import pooch
+from bioio_imageio import Reader as ImageIOReader
+from bioio_ome_tiff import Reader as OmeTiffReader
+
+from ndevio import nImage
+
+if TYPE_CHECKING:
+    from napari.types import LayerDataTuple
+
+SAMPLE_DIR = Path(__file__).parent / "data"
+
+
+def ndev_logo() -> list[LayerDataTuple]:
+    """Load the ndev logo image."""
+    return nImage(
+        SAMPLE_DIR / "ndev-logo.png",
+        reader=ImageIOReader,
+    ).get_layer_data_tuples()
+
+
+def scratch_assay() -> list[LayerDataTuple]:
+    """Load scratch assay data with labeled nuclei and cytoplasm."""
+    scratch_assay_raw_path = pooch.retrieve(
+        url="doi:10.5281/zenodo.17845346/scratch-assay-labeled-10T-2Ch.tiff",
+        known_hash="md5:2b98c4ea18cd741a1545e59855348a2f",
+        fname="scratch-assay-labeled-10T-2Ch.tiff",
+        path=SAMPLE_DIR,
+    )
+    img = nImage(
+        scratch_assay_raw_path,
+        reader=OmeTiffReader,
+    )
+    return img.get_layer_data_tuples(
+        in_memory=True,
+        channel_types={
+            "H3342": "image",
+            "oblique": "image",
+            "nuclei": "labels",
+            "cyto": "labels",
+        },
+        channel_kwargs={
+            "H3342": {"colormap": "cyan"},
+            "oblique": {"colormap": "gray"},
+        },
+    )
+
+
+def neocortex() -> list[LayerDataTuple]:
+    """Load neocortex 3-channel image data."""
+    neocortex_raw_path = pooch.retrieve(
+        url="doi:10.5281/zenodo.17845346/neocortex-3Ch.tiff",
+        known_hash="md5:eadc3fac751052461fb2e5f3c6716afa",
+        fname="neocortex-3Ch.tiff",
+        path=SAMPLE_DIR,
+    )
+    return nImage(
+        neocortex_raw_path,
+        reader=OmeTiffReader,
+    ).get_layer_data_tuples(in_memory=True)
+
+
+def neuron_raw() -> list[LayerDataTuple]:
+    """Load raw neuron 4-channel image data.
+
+    This sample is downloaded from Zenodo if not present locally.
+    """
+    neuron_raw_path = pooch.retrieve(
+        url="doi:10.5281/zenodo.17845346/neuron-4Ch_raw.tiff",
+        known_hash="md5:5d3e42bca2085e8588b6f23cf89ba87c",
+        fname="neuron-4Ch_raw.tiff",
+        path=SAMPLE_DIR,
+    )
+    return nImage(
+        neuron_raw_path,
+        reader=OmeTiffReader,
+    ).get_layer_data_tuples(
+        in_memory=True,
+        layer_type="image",
+        channel_kwargs={
+            "PHALL": {"colormap": "gray"},
+        },
+    )
+
+
+def neuron_labels() -> list[LayerDataTuple]:
+    """Load neuron labels data."""
+    return nImage(
+        SAMPLE_DIR / "neuron-4Ch_labels.tiff",
+        reader=OmeTiffReader,
+    ).get_layer_data_tuples(
+        in_memory=True,
+        layer_type="labels",
+    )
+
+
+def neuron_labels_processed() -> list[LayerDataTuple]:
+    """Load processed neuron labels data."""
+    return nImage(
+        SAMPLE_DIR / "neuron-4Ch_labels_processed.tiff",
+        reader=OmeTiffReader,
+    ).get_layer_data_tuples(
+        in_memory=True,
+        layer_type="labels",
+    )

src/ndevio/widgets/_utilities_container.py

@@ -321,7 +321,7 @@ def _on_batch_complete(self):
         self._set_batch_button_state(running=False)
         self._results.value = (
             "Batch concatenated files in directory."
-            f'\nAt {time.strftime("%H:%M:%S")}'
+            f"\nAt {time.strftime('%H:%M:%S')}"
         )
 
     def _on_batch_error(self, ctx, exception):
@@ -702,7 +702,7 @@ def update_metadata_from_layer(self):
         except AttributeError:
             self._results.value = (
                 "Tried to update metadata, but no layer selected."
-                f'\nAt {time.strftime("%H:%M:%S")}'
+                f"\nAt {time.strftime('%H:%M:%S')}"
             )
         except KeyError:
             scale = selected_layer.scale
@@ -714,7 +714,7 @@ def update_metadata_from_layer(self):
             self._results.value = (
                 "Tried to update metadata, but could only update scale"
                 " because layer not opened with ndevio reader."
-                f'\nAt {time.strftime("%H:%M:%S")}'
+                f"\nAt {time.strftime('%H:%M:%S')}"
             )
 
     def open_images(self):
@@ -855,7 +855,7 @@ def _on_concat_complete(self, save_path: Path) -> None:
         self._progress_bar.value = 1
         self._results.value = (
             f"Saved Concatenated Image: {save_path.name}"
-            f'\nAt {time.strftime("%H:%M:%S")}'
+            f"\nAt {time.strftime('%H:%M:%S')}"
         )
 
     def _on_concat_error(self, exception: Exception) -> None:
@@ -865,7 +865,7 @@ def _on_concat_error(self, exception: Exception) -> None:
         self._progress_bar.value = 0
         self._results.value = (
             f"Error concatenating files: {exception}"
-            f'\nAt {time.strftime("%H:%M:%S")}'
+            f"\nAt {time.strftime('%H:%M:%S')}"
         )
 
     def _build_file_sets(self) -> list[tuple[list[Path], str]]:
@@ -899,7 +899,7 @@ def batch_concatenate_files(self) -> None:
 
         if not file_sets:
             self._results.value = (
-                f'No complete file sets found.\nAt {time.strftime("%H:%M:%S")}'
+                f"No complete file sets found.\nAt {time.strftime('%H:%M:%S')}"
             )
             return
 
@@ -974,15 +974,15 @@ def _on_scene_extracted(self, result: tuple[int, str]) -> None:
         self._progress_bar.value = self._progress_bar.value + 1
         self._results.value = (
             f"Extracted scene {scene_idx}: {scene_name}"
-            f'\nAt {time.strftime("%H:%M:%S")}'
+            f"\nAt {time.strftime('%H:%M:%S')}"
         )
 
     def _on_scenes_complete(self, scenes_list: list, _=None) -> None:
         """Handle completion of all scene extractions."""
         self._progress_bar.label = ""
         self._results.value = (
             f"Saved extracted scenes: {scenes_list}"
-            f'\nAt {time.strftime("%H:%M:%S")}'
+            f"\nAt {time.strftime('%H:%M:%S')}"
         )
 
     def _on_scene_error(self, exc: Exception) -> None:
@@ -991,7 +991,7 @@ def _on_scene_error(self, exc: Exception) -> None:
         self._progress_bar.max = 1
         self._progress_bar.value = 0
         self._results.value = (
-            f'Error extracting scenes: {exc}\nAt {time.strftime("%H:%M:%S")}'
+            f"Error extracting scenes: {exc}\nAt {time.strftime('%H:%M:%S')}"
         )
 
     def canvas_export_figure(self) -> None:
@@ -1000,7 +1000,7 @@ def canvas_export_figure(self) -> None:
             self._results.value = (
                 "Exporting Figure only works in 2D mode."
                 "\nUse Screenshot for 3D figures."
-                f'\nAt {time.strftime("%H:%M:%S")}'
+                f"\nAt {time.strftime('%H:%M:%S')}"
             )
             return
 
@@ -1022,7 +1022,7 @@ def canvas_export_figure(self) -> None:
             f"Exported canvas figure to Figures directory."
             f"\nSaved as {save_name}"
             f"\nWith scale factor of {scale}"
-            f'\nAt {time.strftime("%H:%M:%S")}'
+            f"\nAt {time.strftime('%H:%M:%S')}"
         )
         return
 
@@ -1051,7 +1051,7 @@ def canvas_screenshot(self) -> None:
             f"\nSaved as {save_name}"
             f"\nWith canvas dimensions of {canvas_size}"
             f"\nWith scale factor of {scale}"
-            f'\nAt {time.strftime("%H:%M:%S")}'
+            f"\nAt {time.strftime('%H:%M:%S')}"
         )
         return
 
@@ -1118,7 +1118,7 @@ def _on_layer_save_complete(self, result: None = None) -> None:
         self._results.value = (
             f"Saved {self._layer_save_type}: "
             + str(self._save_name.value)
-            + f'\nAt {time.strftime("%H:%M:%S")}'
+            + f"\nAt {time.strftime('%H:%M:%S')}"
         )
 
     def _on_layer_save_error(self, exc: Exception) -> None:
@@ -1127,5 +1127,5 @@ def _on_layer_save_error(self, exc: Exception) -> None:
         self._progress_bar.max = 1
         self._progress_bar.value = 0
         self._results.value = (
-            f'Error saving layers: {exc}\nAt {time.strftime("%H:%M:%S")}'
+            f"Error saving layers: {exc}\nAt {time.strftime('%H:%M:%S')}"
         )