added dataconfigs for Fiber Seg, LDA Preprocessing + Training / Inference

ark_example.py

@@ -60,15 +60,16 @@ _LICENSE = "https://github.com/angelolab/ark-analysis/blob/main/LICENSE"
 # _URL_REPO = "https://huggingface.co/datasets/angelolab/ark_example"
 
 
-_URL_DATA = {
+_URL_DATA: dict[str, str] = {
     "image_data": "./data/image_data.zip",
     "cell_table": "./data/segmentation/cell_table.zip",
     "deepcell_output": "./data/segmentation/deepcell_output.zip",
     "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",
 }
 
-_URL_DATASET_CONFIGS = {
+_URL_DATASET_CONFIGS: dict[str, dict[str, str]] = {
     "segment_image_data": {"image_data": _URL_DATA["image_data"]},
     "cluster_pixels": {
         "image_data": _URL_DATA["image_data"],
@@ -87,6 +88,18 @@ _URL_DATASET_CONFIGS = {
         "deepcell_output": _URL_DATA["deepcell_output"],
         "example_cell_output_dir": _URL_DATA["example_cell_output_dir"],
     },
+    "fiber_segmentation": {
+        "image_data": _URL_DATA["image_data"],
+    },
+    "LDA_preprocessing": {
+        "image_data": _URL_DATA["image_data"],
+        "cell_table": _URL_DATA["cell_table"],
+    },
+    "LDA_training_inference": {
+        "image_data": _URL_DATA["image_data"],
+        "cell_table": _URL_DATA["cell_table"],
+        "spatial_lda": _URL_DATA["spatial_lda"],
+    }
 }
 
 
@@ -94,7 +107,7 @@ _URL_DATASET_CONFIGS = {
 class ArkExample(datasets.GeneratorBasedBuilder):
     """The Dataset consists of 11 FOVs"""
 
-    VERSION = datasets.Version("0.0.3")
+    VERSION = datasets.Version("0.0.4")
 
     # This is an example of a dataset with multiple configurations.
     # If you don't want/need to define several sub-sets in your dataset,
@@ -126,6 +139,22 @@ class ArkExample(datasets.GeneratorBasedBuilder):
             version=VERSION,
             description="This configuration contains data used by notebook 4 - Post Clustering.",
         ),
+        datasets.BuilderConfig(
+            name="fiber_segmentation",
+            version=VERSION,
+            description="This configuration contains data used by the Fiber Segmentation Notebook.",
+        ),
+        datasets.BuilderConfig(
+            name="LDA_preprocessing",
+            version=VERSION,
+            description="This configuration contains data used by the Spatial LDA - Preprocessing Notebook."
+        ),
+        datasets.BuilderConfig(
+            name="LDA_training_inference",
+            version=VERSION,
+            description="This configuration contains data used by the Spatial LDA - Training and Inference Notebook."
+        ),
+        
     ]
 
     def _info(self):

data/spatial_analysis/spatial_lda.zip

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:7028b6b132fa51eee9ebb99f9f79106e9a6f1505cd92604cc1a6dce6f99aee7a
+size 3486371