diff --git a/Colab_notebooks/Cellpose_2D_ZeroCostDL4Mic.ipynb b/Colab_notebooks/Cellpose_2D_ZeroCostDL4Mic.ipynb index 831929c9..8c67c3ec 100644 --- a/Colab_notebooks/Cellpose_2D_ZeroCostDL4Mic.ipynb +++ b/Colab_notebooks/Cellpose_2D_ZeroCostDL4Mic.ipynb @@ -1239,31 +1239,37 @@ "\n", " print('The model \"Cytoplasm2\" will be evaluated')\n", "\n", - " if model_choice == \"Cytoplasm3\":\n", - " channels=[segment_channel,nuclear_channel]\n", + " if QC_model == \"Cytoplasm3\":\n", " model = models.Cellpose(gpu=True, model_type=\"cyto3\")\n", + " QC_model_folder = Saving_path\n", + " QC_model_name = \"Cytoplasm3\" \n", + "\n", " print(\"Cytoplasm 3 model enabled\")\n", "\n", " if QC_model == \"Cytoplasm2_Omnipose\":\n", " model = models.Cellpose(gpu=True, model_type=\"cyto2_omni\")\n", " QC_model_folder = Saving_path\n", " QC_model_name = \"Cytoplasm2_Omnipose\"\n", + "\n", " print(\"The model Cytoplasm2_Omnipose will be evaluated\")\n", "\n", " if QC_model == \"LiveCell\":\n", - " channels=[segment_channel,0]\n", " model = models.CellposeModel(gpu=True, model_type=\"livecell\")\n", + " QC_model_folder = Saving_path\n", + " QC_model_name = \"LiveCell\" \n", " print(\"LiveCell model enabled\")\n", "\n", " if QC_model == \"Bacteria_Omnipose\":\n", - " channels=[segment_channel,nuclear_channel]\n", " model = models.Cellpose(gpu=True, model_type=\"bact_omni\")\n", " Object_diameter = 0\n", + " QC_model_folder = Saving_path\n", + " QC_model_name = \"Bacteria_Omnipose\" \n", " print(\"Bacteria_omnipose model enabled\")\n", "\n", " if QC_model == \"TissueNet\":\n", - " channels=[segment_channel,nuclear_channel]\n", " model = models.CellposeModel(gpu=True, model_type='tissuenet')\n", + " QC_model_folder = Saving_path\n", + " QC_model_name = \"TissueNet\" \n", " print(\"TissueNet model enabled\")\n", "\n", " if QC_model == \"Nuclei\":\n", @@ -1824,6 +1830,9 @@ "if QC_model == \"Cytoplasm2\":\n", " channels=[segment_channel,nuclear_channel]\n", "\n", + "if QC_model == \"Cytoplasm3\":\n", + " channels=[segment_channel,nuclear_channel] \n", + "\n", "if QC_model == \"Nuclei\":\n", " channels=[segment_channel,0]\n", "\n", @@ -2578,4 +2587,4 @@ }, "nbformat": 4, "nbformat_minor": 0 -} \ No newline at end of file +}