added colon 3d

cns-iu · Jan 9, 2024 · 82016cc · 82016cc
1 parent 71b8768
commit 82016cc
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diff --git a/code_vitessce/docker/samples/commands.txt b/code_vitessce/docker/samples/commands.txt
@@ -50,3 +50,9 @@ python ometif2vitessce.py --IMG_ROOT ./image --OUTPUT_ROOT ./output --OUTPUT_LEV
 
 python ometif2vitessce.py --IMG_ROOT ./image --OUTPUT_ROOT ./output --OUTPUT_LEVEL 0 --DATA_SOURCE NET --INFO_CSV ./info.csv --COLOR_SCHEME_CSV "https://storagetuzi.blob.core.windows.net/blobtuzi/gloria/cell_sets.csv" --PROJECT_NAME GLORIA
 
+# colon_3d
+
+python ometif2vitessce.py --IMG_ROOT ./image --OUTPUT_ROOT ./output --OUTPUT_LEVEL 0 --DATA_SOURCE NET --INFO_CSV ./info.csv --COLOR_SCHEME_CSV "# gloria
+
+python ometif2vitessce.py --IMG_ROOT ./image --OUTPUT_ROOT ./output --OUTPUT_LEVEL 0 --DATA_SOURCE NET --INFO_CSV ./info.csv --COLOR_SCHEME_CSV "https://storagetuzi.blob.core.windows.net/blobtuzi/gloria/cell_sets.csv" --PROJECT_NAME GLORIA
+" --PROJECT_NAME COLON_3D
diff --git a/code_vitessce/docker/utils/info_csv_generator_colon3d.py b/code_vitessce/docker/utils/info_csv_generator_colon3d.py
@@ -3,7 +3,7 @@
 
 # Given data
 image_urls = [
-    rf'https://storagetuzi.blob.core.windows.net/blobtuzi/gloria/Region_D265_mask.pyramid.ome.tif']
+    rf'https://storagetuzi.blob.core.windows.net/blobtuzi/colon_3d/Region_CRC01050_mask.pyramid.ome.tif']
 
 region_names = [f"CRC01050"]
 rows = len(region_names)