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HenriquesLab · Apr 25, 2024 · 87f77f7 · 87f77f7
1 parent c7f0eec
commit 87f77f7
Showing 1 changed file with 12 additions and 8 deletions.
diff --git a/Colab_notebooks/Cellpose_2D_ZeroCostDL4Mic.ipynb b/Colab_notebooks/Cellpose_2D_ZeroCostDL4Mic.ipynb
@@ -2071,24 +2071,24 @@
         "\n",
         "#@markdown ###What model do you want to use?\n",
         "\n",
-        "model_choice = \"Cytoplasm\" #@param [\"Cytoplasm\",\"Cytoplasm2\",\"LiveCell\", \"TissueNet\", \"Cytoplasm2_Omnipose\", \"Bacteria_Omnipose\", \"Nuclei\", \"Own_model\"]\n",
+        "model_choice = \"Cytoplasm3\" #@param [\"Cytoplasm\",\"Cytoplasm2\",\"Cytoplasm3\",\"LiveCell\", \"TissueNet\", \"Cytoplasm2_Omnipose\", \"Bacteria_Omnipose\", \"Nuclei\", \"Own_model\"]\n",
         "\n",
         "#@markdown ####If using your own model, please provide the path to the model (not the folder):\n",
         "\n",
         "Prediction_model = \"\" #@param {type:\"string\"}\n",
         "\n",
         "#@markdown ### What channel do you want to segment?\n",
         "\n",
-        "Channel_to_segment= \"Grayscale\" #@param [\"Grayscale\", \"Blue\", \"Green\", \"Red\"]\n",
+        "Channel_to_segment= \"Red\" #@param [\"Grayscale\", \"Blue\", \"Green\", \"Red\"]\n",
         "\n",
         "# @markdown ###If you chose the model \"cytoplasm\" indicate if you also have a nuclear channel that can be used to aid the segmentation.\n",
         "\n",
-        "Nuclear_channel= \"None\" #@param [\"None\", \"Blue\", \"Green\", \"Red\"]\n",
+        "Nuclear_channel= \"Blue\" #@param [\"None\", \"Blue\", \"Green\", \"Red\"]\n",
         "\n",
         "#@markdown ### Segmentation parameters:\n",
-        "Object_diameter =  0#@param {type:\"number\"}\n",
+        "Object_diameter =  500#@param {type:\"number\"}\n",
         "\n",
-        "Flow_threshold = 0.1 #@param {type:\"slider\", min:0.0, max:3, step:0.1}\n",
+        "Flow_threshold = 1.5 #@param {type:\"slider\", min:0.0, max:3, step:0.1}\n",
         "\n",
         "mask_threshold=0 #@param {type:\"slider\", min:-6, max:6, step:1}\n",
         "\n",
@@ -2131,6 +2131,11 @@
         "  model = models.Cellpose(gpu=True, model_type=\"cyto\")\n",
         "  print(\"Cytoplasm model enabled\")\n",
         "\n",
+        "if model_choice == \"Cytoplasm3\":\n",
+        "  channels=[segment_channel,nuclear_channel]\n",
+        "  model = models.Cellpose(gpu=True, model_type=\"cyto3\")\n",
+        "  print(\"Cytoplasm 3 model enabled\")\n",
+        "\n",
         "if model_choice == \"Cytoplasm2\":\n",
         "  channels=[segment_channel,nuclear_channel]\n",
         "  model = models.Cellpose(gpu=True, model_type=\"cyto2\")\n",
@@ -2564,8 +2569,7 @@
     "accelerator": "GPU",
     "colab": {
       "machine_shape": "hm",
-      "provenance": [],
-      "toc_visible": true
+      "provenance": []
     },
     "kernelspec": {
       "display_name": "Python 3",
@@ -2586,4 +2590,4 @@
   },
   "nbformat": 4,
   "nbformat_minor": 0
-}
+}