update cell segmentation tutorials

STOmics · Apr 28, 2023 · 6e86f72 · 6e86f72
1 parent bc7b3a2
commit 6e86f72
Showing 1 changed file with 12 additions and 12 deletions.
diff --git a/docs/source/Tutorials/Cell_Segmentation.ipynb b/docs/source/Tutorials/Cell_Segmentation.ipynb
@@ -128,10 +128,10 @@
    "source": [
     "from stereo import image as im\n",
     "\n",
-    "model_path = '/ldfssz1/ST_BI/USER/stereopy/test/lyonlin/test_cell_seg/cell_segmetation_v3.0.onnx'\n",
-    "img_path = '/ldfssz1/ST_BI/USER/stereopy/test/lyonlin/test_cell_seg/SS200000135TL_D1_regist.tif'\n",
-    "out_path = '/ldfssz1/ST_BI/USER/stereopy/test/lyonlin/test_cell_seg/cell_seg_res/SS200000135TL_D1_regist.cell_cut.tif'\n",
-    "tissue_seg_model_path = \"/ldfssz1/ST_BI/USER/tangdecong/database/stereopy_model/weight_tissue_cut_tool_220304.hdf5\"\n",
+    "model_path = './cell_segmetation_v3.0.onnx'\n",
+    "img_path = './SS200000135TL_D1_regist.tif'\n",
+    "out_path = './SS200000135TL_D1_regist.cell_cut.tif'\n",
+    "tissue_seg_model_path = \"./weight_tissue_cut_tool_220304.hdf5\"\n",
     "tissue_seg_method = 1\n",
     "\n",
     "im.cell_seg_v3(model_path, img_path, out_path, need_tissue_cut=True, tissue_seg_model_path=tissue_seg_model_path, tissue_seg_method=1)"
@@ -206,10 +206,10 @@
    "source": [
     "from stereo import image as im\n",
     "\n",
-    "model_path = '/ldfssz1/ST_BI/USER/stereopy/test/lyonlin/test_cell_seg/seg_model_20211210.pth'\n",
-    "img_path = '/ldfssz1/ST_BI/USER/stereopy/test/lyonlin/test_cell_seg/SS200000135TL_D1_regist.tif'\n",
-    "out_path = '/ldfssz1/ST_BI/USER/stereopy/test/lyonlin/test_cell_seg/cell_seg_res/'\n",
-    "tissue_seg_model_path = \"/ldfssz1/ST_BI/USER/tangdecong/database/stereopy_model/weight_tissue_cut_tool_220304.hdf5\"\n",
+    "model_path = './seg_model_20211210.pth'\n",
+    "img_path = './SS200000135TL_D1_regist.tif'\n",
+    "out_path = './cell_seg_res/'\n",
+    "tissue_seg_model_path = \"./weight_tissue_cut_tool_220304.hdf5\"\n",
     "tissue_seg_method = 1\n",
     "\n",
     "im.cell_seg(model_path, img_path, out_path, tissue_seg_model_path=tissue_seg_model_path, tissue_seg_method=1)"
@@ -284,10 +284,10 @@
     }
    ],
    "source": [
-    "model_dir = '/ldfssz1/ST_BI/USER/stereopy/test/lyonlin/test_cell_seg/cell_segmentation_deepcell/'\n",
-    "img_path = '/ldfssz1/ST_BI/USER/stereopy/test/lyonlin/test_cell_seg/SS200000135TL_D1_regist.tif'\n",
-    "out_path = '/ldfssz1/ST_BI/USER/stereopy/test/lyonlin/test_cell_seg/cell_seg_res/deepcell/'\n",
-    "tissue_seg_model_path = \"/ldfssz1/ST_BI/USER/tangdecong/database/stereopy_model/weight_tissue_cut_tool_220304.hdf5\"\n",
+    "model_dir = './cell_segmentation_deepcell/'\n",
+    "img_path = './SS200000135TL_D1_regist.tif'\n",
+    "out_path = './deepcell/'\n",
+    "tissue_seg_model_path = \"./weight_tissue_cut_tool_220304.hdf5\"\n",
     "tissue_seg_method = 1\n",
     "\n",
     "im.cell_seg_deepcell(model_dir, img_path, out_path, tissue_seg_model_path=tissue_seg_model_path, tissue_seg_method=1)"