OME-TIFF Example File

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"],
+    },
 }
 
 
@@ -117,7 +121,7 @@ _URL_DATASET_CONFIGS = {
 class ArkExample(datasets.GeneratorBasedBuilder):
     """The Dataset consists of 11 FOVs"""
 
-    VERSION = datasets.Version("0.0.4")
+    VERSION = datasets.Version("0.0.5")
 
     # You will be able to load one or the other configurations in the following list with
     BUILDER_CONFIGS = [
@@ -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/image_data.zip

@@ -1,3 +1,3 @@
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-size 400230929
+oid sha256:4d1f29e53a40bb162e795f68906095131d88647f70a6e080ca3bac749a3f6174
+size 373529148

data/ome_tiff.zip

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

data/pixie/example_cell_output_dir.zip

@@ -1,3 +1,3 @@
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-size 86425942
+oid sha256:cc349ee903cad26027b57eb7437bc8a102ef82b6de1a72cfd98f71894b95132f
+size 2873164

data/pixie/example_pixel_output_dir.zip

@@ -1,3 +1,3 @@
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-size 1494869638
+oid sha256:52ba294101b827288bc0ceb2575dad63149989798bed91efe6f9c33541185436
+size 1384925341

data/post_clustering.zip

@@ -1,3 +1,3 @@
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-size 9720247
+oid sha256:d969d298c2a42130f17955b13f5b1b2c1e8687c180e1e27ce9205bc9ea8d33a1
+size 9209730

data/segmentation/cell_table.zip

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-size 15162294
+oid sha256:b4be2617f5ac13fc27a70ee949578d985fa03721df1f508d697a0d9404ff8c18
+size 14370520

data/segmentation/deepcell_output.zip

@@ -1,3 +1,3 @@
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-size 1552324
+oid sha256:92c1bf023c58187264d31848addb602d8aeb7f7545ef0fa370c73a5f35325a15
+size 1571004

data/spatial_analysis/spatial_lda.zip

@@ -1,3 +1,3 @@
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-size 3486371
+oid sha256:eb7bdab9c054d4fff8504c51e9b185e02a8cc13e15287bafdee2fbb7ddcd66b4
+size 3296785