OME-TIFF Example File (#10)

- added ome_tiff example, added config to ark_example.py (bc1594eae91694a7eb41ca148807ee6cda389f28)
- put ome tiff in folder (0b953f29ca3b22880c9c21424cfa4429ad8b2e8f)
- Merge branch 'main' into pr/10 (b5264333585ea06ec80593a2e1355e439f943dbd)
- Merge branch 'main' into pr/10 (a436d9b53e736c60066ff260d81a1b52eb079e87)
- Merge branch 'main' into pr/10 (c7f356e3e7139d31f132cff282695629c48edf28)

ark_example.py

@@ -65,7 +65,8 @@ _URL_DATA = {
     "example_pixel_output_dir": "./data/pixie/example_pixel_output_dir.zip",
     "example_cell_output_dir": "./data/pixie/example_cell_output_dir.zip",
     "spatial_lda": "./data/spatial_analysis/spatial_lda.zip",
-    "post_clustering": "./data/post_clustering.zip"
+    "post_clustering": "./data/post_clustering.zip",
+    "ome_tiff": "./data/ome_tiff.zip",
 }
 
 _URL_DATASET_CONFIGS = {
@@ -109,7 +110,10 @@ _URL_DATASET_CONFIGS = {
         "cell_table": _URL_DATA["cell_table"],
         "deepcell_output": _URL_DATA["deepcell_output"],
         "post_clustering": _URL_DATA["post_clustering"],
-    }
+    },
+    "ome_tiff": {
+        "ome_tiff": _URL_DATA["ome_tiff"],
+    },
 }
 
 
@@ -165,22 +169,17 @@ class ArkExample(datasets.GeneratorBasedBuilder):
             name="pairwise_spatial_enrichment",
             version=VERSION,
             description="This configuration contains data used by the Pairwise Spatial Enrichment Notebook."
+        ),
+        datasets.BuilderConfig(
+            name="ome_tiff",
+            version=VERSION,
+            description="This configuration contains an OME-TIFF format of FOV1. Intended to be used with the OME-TIFF Conversion Notebook."
         )
     ]
 
     def _info(self):
         # This is the name of the configuration selected in BUILDER_CONFIGS above
-        if self.config.name in [
-            "segment_image_data",
-            "cluster_pixels",
-            "cluster_cells",
-            "post_clustering",
-            "fiber_segmentation",
-            "LDA_preprocessing",
-            "LDA_training_inference",
-            "neighborhood_analysis",
-            "pairwise_spatial_enrichment",
-        ]:
+        if self.config.name in list(_URL_DATASET_CONFIGS.keys()):
             features = datasets.Features(
                 {f: datasets.Value("string") for f in _URL_DATASET_CONFIGS[self.config.name].keys()}
             )

data/ome_tiff.zip

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:82d3278f7d3e27e128f3ec3607934b933f68e3a3aab1298ce1e6dc5d0cf402e2
+size 37043244