constrain cellpose version to v2.3.2

pr4deepr · Apr 9, 2024 · a8b5ca8 · a8b5ca8
1 parent 6c68cea
commit a8b5ca8
Showing 1 changed file with 11 additions and 4 deletions.
diff --git a/Cellpose_cell_segmentation_2D_prediction_only.ipynb b/Cellpose_cell_segmentation_2D_prediction_only.ipynb
@@ -42,7 +42,7 @@
         "id": "Nb90LCrotIx4"
       },
       "source": [
-        "#**Cellpose Prediction for 2D v0.4**\n",
+        "#**Cellpose Prediction for 2D v0.5**\n",
         "A generalist algorithm for cell and nucleus segmentation.\n",
         "\n",
         "***Cellpose code: Carsen Stringer & Marius Pachitariu***\n",
@@ -61,6 +61,13 @@
         "\n",
         "I have only tested it on jpg and tiff files. Feel free to email me if you have any questions.\n",
         "\n",
+        "**This notebook uses cellpose v2.3.2.**\n",
+        "\n",
+        "v0.5 update:\n",
+        "\n",
+        "* 2024/04/09 Constrained cellpose version to be 2.3.2 to maintain compatibility.\n",
+        "\n",
+        "\n",
         "v0.4 update:\n",
         "\n",
         "* Fixed bug where new models could not be used for prediction\n",
@@ -183,7 +190,7 @@
         "\n",
         "#@markdown * On occasion, you may not be able to see the folders on the left panel. Just refresh your browser webpage and it should appear.\n",
         "#!pip install git+https://www.github.com/mouseland/cellpose.git #to install development version\n",
-        "!pip install cellpose\n",
+        "!pip install \"cellpose==2.3.2\"\n",
         "!pip install torch torchvision torchaudio\n",
         "!pip install omnipose\n",
         "\n",
@@ -279,7 +286,7 @@
         "\n",
         "#@markdown ###Optional: Enter image extension here to read only files/images of specified extension (.tif,.jpg..):\n",
         "#@markdown ###### Leave empty if not specifying anything\n",
-        "image_format = \"jpg\" #@param {type:\"string\"}\n",
+        "image_format = \"png\" #@param {type:\"string\"}\n",
         "\n",
         "##@markdown ###Tick if image is RGB:\n",
         "#RGB= False #@param {type:\"boolean\"}\n",
@@ -457,7 +464,7 @@
         "\n",
         "# @markdown ###If you choose cytoplasm, tick if you have a nuclear channel\n",
         "Use_nuclear_channel= True #@param {type:\"boolean\"}\n",
-        "Nuclear_channel=\"2\" #@param[1,2,3,4,5]\n",
+        "Nuclear_channel=\"3\" #@param[1,2,3,4,5]\n",
         "nuclear_channel=int(Nuclear_channel)\n",
         "\n",
         "# @markdown ###If cells are elongated or have branches, tick this. It will use omnipose\n",