datasets for downloading example data

docs/api.rst

@@ -319,6 +319,15 @@ Utilities specifically for stitching operations.
     scallops.stitch.utils.tile_overlap_mask
 
 
+Datasets
+===================
+Builtin datasets for testing
+
+.. autosummary::
+    :toctree: .
+
+    scallops.datasets.example_feature_summary_stats
+    scallops.datasets.feldman_2019_small
 
 .. _`SKimage' phase cross correlation`: https://scikit-image.org/docs/stable/api/skimage.registration.html#skimage.registration.phase_cross_correlation
 .. _ITK: https://itk.org/Doxygen/html/RegistrationPage.html

scallops/datasets/__init__.py

@@ -0,0 +1,65 @@
+from pathlib import Path
+
+
+def example_feature_summary_stats() -> Path:
+    """Example phenotype feature summary statistics.
+
+    :return: Path to Parquet file.
+    """
+    import pooch
+
+    registry = {
+        "features/plotting-notebook-example-summary-stats.pq": None,
+    }
+    path = pooch.os_cache("scallops")
+    p = pooch.create(
+        path=path,
+        base_url="https://github.com/Genentech/scallops/raw/refs/heads/main/scallops/tests/data/",
+        registry=registry,
+    )
+    for key in registry.keys():
+        p.fetch(key)
+    return path / "features" / "plotting-notebook-example-summary-stats.pq"
+
+
+def feldman_2019_small() -> Path:
+    """Example SBS and phenotype tiles from Optical Pooled Screens in Human Cells
+    by Feldman et al. (https://www.cell.com/cell/fulltext/S0092-8674(19)31067-0).
+
+    :return: Path to root data directory.
+    """
+
+    import pooch
+
+    registry = {
+        "experimentC/input/10X_c10-SBS-10/10X_c10-SBS-10_A1_Tile-102.sbs.tif": None,
+        "experimentC/input/10X_c10-SBS-10/10X_c10-SBS-10_A1_Tile-103.sbs.tif": None,
+        "experimentC/input/10X_c1-SBS-1/10X_c1-SBS-1_A1_Tile-103.sbs.tif": None,
+        "experimentC/input/10X_c1-SBS-1/10X_c1-SBS-1_A1_Tile-102.sbs.tif": None,
+        "experimentC/input/10X_c7-SBS-7/10X_c7-SBS-7_A1_Tile-102.sbs.tif": None,
+        "experimentC/input/10X_c7-SBS-7/10X_c7-SBS-7_A1_Tile-103.sbs.tif": None,
+        "experimentC/input/10X_c2-SBS-2/10X_c2-SBS-2_A1_Tile-102.sbs.tif": None,
+        "experimentC/input/10X_c2-SBS-2/10X_c2-SBS-2_A1_Tile-103.sbs.tif": None,
+        "experimentC/input/10X_c9-SBS-9/10X_c9-SBS-9_A1_Tile-103.sbs.tif": None,
+        "experimentC/input/10X_c9-SBS-9/10X_c9-SBS-9_A1_Tile-102.sbs.tif": None,
+        "experimentC/input/10X_c4-SBS-4/10X_c4-SBS-4_A1_Tile-103.sbs.tif": None,
+        "experimentC/input/10X_c4-SBS-4/10X_c4-SBS-4_A1_Tile-102.sbs.tif": None,
+        "experimentC/input/10X_c3-SBS-3/10X_c3-SBS-3_A1_Tile-103.sbs.tif": None,
+        "experimentC/input/10X_c3-SBS-3/10X_c3-SBS-3_A1_Tile-102.sbs.tif": None,
+        "experimentC/input/10X_c8-SBS-8/10X_c8-SBS-8_A1_Tile-102.sbs.tif": None,
+        "experimentC/input/10X_c8-SBS-8/10X_c8-SBS-8_A1_Tile-103.sbs.tif": None,
+        "experimentC/input/10X_c5-SBS-5/10X_c5-SBS-5_A1_Tile-102.sbs.tif": None,
+        "experimentC/input/10X_c5-SBS-5/10X_c5-SBS-5_A1_Tile-103.sbs.tif": None,
+        "experimentC/10X_c0-DAPI-p65ab/10X_c0-DAPI-p65ab_A1_Tile-103.phenotype.tif": None,
+        "experimentC/10X_c0-DAPI-p65ab/10X_c0-DAPI-p65ab_A1_Tile-102.phenotype.tif": None,
+        "experimentC/barcodes.csv": None,
+    }
+    path = pooch.os_cache("scallops")
+    p = pooch.create(
+        path=path,
+        base_url="https://github.com/Genentech/scallops/raw/refs/heads/main/scallops/tests/data/",
+        registry=registry,
+    )
+    for key in registry.keys():
+        p.fetch(key)
+    return path / "experimentC"

scallops/visualize/registration.py

@@ -148,7 +148,7 @@ def plot_registration(
             )
             plt.show()
     """
-    stacks = [x.isel(z=0).squeeze() for x in stacks]
+    stacks = [x.isel(z=0, missing_dims="ignore").squeeze() for x in stacks]
     axes = None
     all_rounds = [stack.coords["t"].values for stack in stacks]
     assert all(array_equal(all_rounds[0], x) for x in all_rounds), (