AlexEMG · Oct 1, 2025 · Sep 4, 2025 · Sep 4, 2025 · Sep 4, 2025 · Sep 4, 2025
diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
@@ -13,12 +13,12 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-14, windows-latest]
-        python-version: ["3.10"]
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.10", "3.11", "3.12"]
         include:
           - os: ubuntu-latest
             path: ~/.cache/pip
-          - os: macos-14
+          - os: macos-latest
             path: ~/Library/Caches/pip
           - os: windows-latest
             path: ~\AppData\Local\pip\Cache
@@ -38,18 +38,13 @@ jobs:
         shell: bash -el {0}  # Important: activates the conda environment
         if: runner.os != 'macOS'
         run: |
-          pip install tensorflow==2.12.0 tensorpack==0.11 tf_slim==1.1.0
+          pip install tensorflow tensorpack==0.11 tf_slim==1.1.0 tf-keras
 
       - name: Install TensorFlow on macOS
         shell: bash -el {0}  # Important: activates the conda environment
         if: runner.os == 'macOS'
         run: |
-          pip install tensorflow-macos==2.12.0 tensorpack==0.11 tf_slim==1.1.0
-
-      - name: Install PyTables through Conda
-        shell: bash -el {0}  # Important: activates the conda environment
-        run: |
-          conda install pytables==3.8.0 "numpy<2"
+          pip install tensorflow-macos tensorpack==0.11 tf_slim==1.1.0 tf-keras
 
       - name: Install dependencies
         shell: bash -el {0}  # Important: activates the conda environment

diff --git a/deeplabcut/pose_estimation_tensorflow/__init__.py b/deeplabcut/pose_estimation_tensorflow/__init__.py
@@ -12,6 +12,8 @@
 # Licensed under GNU Lesser General Public License v3.0
 #
 
+from . import _tf_legacy
+
 # Suppress tensorflow warning messages
 import tensorflow as tf
 tf.compat.v1.logging.set_verbosity(tf.compat.v1.logging.ERROR)

diff --git a/deeplabcut/pose_estimation_tensorflow/_tf_legacy.py b/deeplabcut/pose_estimation_tensorflow/_tf_legacy.py
@@ -0,0 +1,12 @@
+import os
+import sys
+
+os.environ.setdefault("TF_USE_LEGACY_KERAS", "1")
+os.environ.setdefault("WRAPT_DISABLE_EXTENSIONS", "1")
+
+try:
+    import tf_keras.src.legacy_tf_layers as legacy_tf_layers
+    sys.modules["tf_keras.legacy_tf_layers"] = legacy_tf_layers
+except ImportError:
+    # Older tf-keras didn’t use src/, so nothing to do
+    pass
diff --git a/examples/COLAB/COLAB_3miceDemo.ipynb b/examples/COLAB/COLAB_3miceDemo.ipynb
@@ -36,32 +36,7 @@
     "- a quick guide to maDLC: https://deeplabcut.github.io/DeepLabCut/docs/tutorial.html\n",
     "- a demo COLAB for how to use maDLC on your own data: https://github.com/DeepLabCut/DeepLabCut/blob/main/examples/COLAB/COLAB_maDLC_TrainNetwork_VideoAnalysis.ipynb\n",
     "\n",
-    "### To get started, please go to \"Runtime\" ->\"change runtime type\"->select \"Python3\", and then select \"GPU\"\n",
-    "\n",
-    "As the COLAB environments were updated to CUDA 12.X and Python 3.11, we need to install DeepLabCut and TensorFlow in a distinct way to get TensorFlow to connect to the GPU."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "id": "HoNN2_0Z9rr_"
-   },
-   "outputs": [],
-   "source": [
-    "# Install TensorFlow, tensorpack and tf_slim versions compatible with DeepLabCut\n",
-    "!pip install \"tensorflow==2.12.1\" \"tensorpack>=0.11\" \"tf_slim>=1.1.0\""
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Downgrade PyTorch to a version using CUDA 11.8 and cudnn 8\n",
-    "# This will also install the required CUDA libraries, for both PyTorch and TensorFlow\n",
-    "!pip install torch==2.3.1 torchvision --index-url https://download.pytorch.org/whl/cu118"
+    "### To get started, please go to \"Runtime\" ->\"change runtime type\"->select \"Python3\", and then select \"GPU\""
    ]
   },
   {
@@ -71,18 +46,7 @@
    "outputs": [],
    "source": [
     "# Install the correct (older) version of DeepLabCut\n",
-    "!pip install deeplabcut==2.3.11"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# As described in https://www.tensorflow.org/install/pip#step-by-step_instructions, \n",
-    "# create symbolic links to NVIDIA shared libraries:\n",
-    "!ln -svf /usr/local/lib/python3.11/dist-packages/nvidia/*/lib/*.so* /usr/local/lib/python3.11/dist-packages/tensorflow"
+    "!pip install \"deeplabcut[tf]\""
    ]
   },
   {

diff --git a/examples/COLAB/COLAB_DLC_ModelZoo.ipynb b/examples/COLAB/COLAB_DLC_ModelZoo.ipynb
@@ -45,30 +45,7 @@
         "\n",
         "## **Let's get going: install DeepLabCut into COLAB:**\n",
         "\n",
-        "*Also, be sure you are connected to a GPU: go to menu, click Runtime > Change Runtime Type > select \"GPU\"*\n",
-        "\n",
-        "As the COLAB environments were updated to CUDA 12.X and Python 3.11, we need to install DeepLabCut and TensorFlow in a distinct way to get TensorFlow to connect to the GPU."
-      ]
-    },
-    {
-      "cell_type": "code",
-      "execution_count": null,
-      "metadata": {},
-      "outputs": [],
-      "source": [
-        "# Install TensorFlow, tensorpack and tf_slim versions compatible with DeepLabCut\n",
-        "!pip install \"tensorflow==2.12.1\" \"tensorpack>=0.11\" \"tf_slim>=1.1.0\""
-      ]
-    },
-    {
-      "cell_type": "code",
-      "execution_count": null,
-      "metadata": {},
-      "outputs": [],
-      "source": [
-        "# Downgrade PyTorch to a version using CUDA 11.8 and cudnn 8\n",
-        "# This will also install the required CUDA libraries, for both PyTorch and TensorFlow\n",
-        "!pip install torch==2.3.1 torchvision --index-url https://download.pytorch.org/whl/cu118"
+        "*Also, be sure you are connected to a GPU: go to menu, click Runtime > Change Runtime Type > select \"GPU\"*\n"
       ]
     },
     {
@@ -78,18 +55,7 @@
       "outputs": [],
       "source": [
         "# Install the latest version of DeepLabCut\n",
-        "!pip install \"git+https://github.com/DeepLabCut/DeepLabCut.git#egg=deeplabcut[modelzoo]\""
-      ]
-    },
-    {
-      "cell_type": "code",
-      "execution_count": null,
-      "metadata": {},
-      "outputs": [],
-      "source": [
-        "# As described in https://www.tensorflow.org/install/pip#step-by-step_instructions, \n",
-        "# create symbolic links to NVIDIA shared libraries:\n",
-        "!ln -svf /usr/local/lib/python3.11/dist-packages/nvidia/*/lib/*.so* /usr/local/lib/python3.11/dist-packages/tensorflow"
+        "!pip install --pre \"deeplabcut[tf,modelzoo]\""
       ]
     },
     {

diff --git a/examples/COLAB/COLAB_transformer_reID.ipynb b/examples/COLAB/COLAB_transformer_reID.ipynb
@@ -32,91 +32,18 @@
         "- a quick guide to maDLC: https://deeplabcut.github.io/DeepLabCut/docs/tutorial.html\n",
         "- a demo COLAB for how to use maDLC on your own data: https://github.com/DeepLabCut/DeepLabCut/blob/main/examples/COLAB/COLAB_maDLC_TrainNetwork_VideoAnalysis.ipynb\n",
         "\n",
-        "### To get started, please go to \"Runtime\" ->\"change runtime type\"->select \"Python3\", and then select \"GPU\"\n",
-        "\n",
-        "As the COLAB environments were updated to CUDA 12.X and Python 3.11, we need to install DeepLabCut and TensorFlow in a distinct way to get TensorFlow to connect to the GPU."
+        "### To get started, please go to \"Runtime\" ->\"change runtime type\"->select \"Python3\", and then select \"GPU\"\n"
       ]
     },
     {
       "cell_type": "markdown",
       "source": [
-        "‼️ **Attention: this demo is for maDLC, which is version 2.2**\n",
-        "- the installation is very slow on Colab due to the several steps needed to use older versions of `torch` and `dlc`."
+        "‼️ **Attention: this demo is for maDLC, which is version 2.2**\n"
       ],
       "metadata": {
         "id": "xOe2hvy85EVP"
       }
     },
-    {
-      "cell_type": "code",
-      "execution_count": null,
-      "metadata": {
-        "id": "6_Q4_GKM45Oe"
-      },
-      "outputs": [],
-      "source": [
-        "# Downgrade PyTorch to a version using CUDA 11.8 and cudnn 8\n",
-        "# This will also install the required CUDA libraries, for both PyTorch and TensorFlow\n",
-        "!pip install torch==2.3.1 torchvision --index-url https://download.pytorch.org/whl/cu118"
-      ]
-    },
-    {
-      "cell_type": "code",
-      "source": [
-        "import torch\n",
-        "print(torch.cuda.is_available())\n",
-        "print(torch.cuda.get_device_name(0))\n",
-        "!nvcc --version  # sometimes not available"
-      ],
-      "metadata": {
-        "colab": {
-          "base_uri": "https://localhost:8080/"
-        },
-        "id": "3HLeBRGL9jYJ",
-        "outputId": "b8e49307-f51c-4f12-8dec-d2c2929928e2"
-      },
-      "execution_count": 3,
-      "outputs": [
-        {
-          "output_type": "stream",
-          "name": "stdout",
-          "text": [
-            "True\n",
-            "NVIDIA A100-SXM4-40GB\n",
-            "nvcc: NVIDIA (R) Cuda compiler driver\n",
-            "Copyright (c) 2005-2024 NVIDIA Corporation\n",
-            "Built on Thu_Jun__6_02:18:23_PDT_2024\n",
-            "Cuda compilation tools, release 12.5, V12.5.82\n",
-            "Build cuda_12.5.r12.5/compiler.34385749_0\n"
-          ]
-        }
-      ]
-    },
-    {
-      "cell_type": "code",
-      "execution_count": null,
-      "metadata": {
-        "id": "Vz3B6Zyf45Od"
-      },
-      "outputs": [],
-      "source": [
-        "# Install TensorFlow, tensorpack and tf_slim versions compatible with DeepLabCut\n",
-        "!pip install \"tensorflow==2.12.1\" \"tensorpack>=0.11\" \"tf_slim>=1.1.0\""
-      ]
-    },
-    {
-      "cell_type": "code",
-      "execution_count": null,
-      "metadata": {
-        "id": "UUpac75T45Of"
-      },
-      "outputs": [],
-      "source": [
-        "# As described in https://www.tensorflow.org/install/pip#step-by-step_instructions,\n",
-        "# create symbolic links to NVIDIA shared libraries:\n",
-        "!ln -svf /usr/local/lib/python3.11/dist-packages/nvidia/*/lib/*.so* /usr/local/lib/python3.11/dist-packages/tensorflow"
-      ]
-    },
     {
       "cell_type": "code",
       "execution_count": null,
@@ -126,15 +53,13 @@
       "outputs": [],
       "source": [
         "# Install DLC version 2.2-2.3 (pre DLC3):\n",
-        "!pip install deeplabcut==2.3.11"
+        "!pip install \"deeplabcut[tf]\""
       ]
     },
     {
       "cell_type": "code",
       "source": [
-        "import tensorflow\n",
         "import deeplabcut\n",
-        "import torch\n",
         "import os"
       ],
       "metadata": {
@@ -143,33 +68,6 @@
       "execution_count": 3,
       "outputs": []
     },
-    {
-      "cell_type": "code",
-      "source": [
-        "print(\"DLC version: \", deeplabcut.__version__)\n",
-        "print(\"torch version: \",torch.__version__)\n",
-        "print(\"tensorflow version: \",tensorflow.__version__)\n"
-      ],
-      "metadata": {
-        "colab": {
-          "base_uri": "https://localhost:8080/"
-        },
-        "id": "wRojzQO98X2H",
-        "outputId": "fad889d6-15da-4888-8138-283f1f13cf99"
-      },
-      "execution_count": 4,
-      "outputs": [
-        {
-          "output_type": "stream",
-          "name": "stdout",
-          "text": [
-            "DLC version:  2.3.11\n",
-            "torch version:  2.3.1+cu118\n",
-            "tensorflow version:  2.12.1\n"
-          ]
-        }
-      ]
-    },
     {
       "cell_type": "markdown",
       "metadata": {

diff --git a/examples/testscript_pytorch_multi_animal.py b/examples/testscript_pytorch_multi_animal.py
@@ -64,12 +64,14 @@ def main(
                     "train_settings.display_iters": 50,
                     "train_settings.epochs": epochs_,
                     "train_settings.batch_size": batch_size,
+                    "train_settings.dataloader_workers": 0,
                     "runner.device": device,
                     "runner.snapshots.save_epochs": save_epochs,
                     "runner.snapshots.max_snapshots": max_snapshots_to_keep,
                     "detector.train_settings.display_iters": 1,
                     "detector.train_settings.epochs": detector_epochs,
                     "detector.train_settings.batch_size": detector_batch_size,
+                    "detector.train_settings.dataloader_workers": 0,
                     "detector.runner.snapshots.save_epochs": save_epochs,
                     "detector.runner.snapshots.max_snapshots": max_snapshots_to_keep,
                     "logger": logger,

diff --git a/requirements.txt b/requirements.txt
@@ -24,7 +24,7 @@ scikit-image>=0.17
 scikit-learn>=1.0
 scipy>=1.9
 statsmodels>=0.11
-tables==3.8.0
+tables
 torch==2.7.1
 torchvision
 tqdm
diff --git a/setup.py b/setup.py
@@ -78,23 +78,26 @@ def pytorch_config_paths() -> list[str]:
         "pycocotools",
         "pyyaml",
         "Pillow>=7.1",
+        "tables",
     ],
     extras_require={
         "gui": [
-            "pyside6==6.4.2",
+            "pyside6",
             "qdarkstyle==3.1",
             "napari-deeplabcut>=0.2.1.6",
         ],
         "openvino": ["openvino-dev==2022.1.0"],
         "docs": ["numpydoc"],
         "tf": [
             "tensorflow>=2.0,<=2.10;platform_system=='Windows'",
-            "tensorflow>=2.0,<=2.12;platform_system!='Windows'",
+            "tensorflow>=2.0;platform_system!='Windows'",
+            "tf-keras;platform_system!='Windows'",
             "tensorpack>=0.11",
             "tf_slim>=1.1.0",
         ],  # Last supported TF version on Windows Native is 2.10
         "apple_mchips": [
-            "tensorflow-macos<2.13.0",
+            "tensorflow-macos",
+            "tf-keras",
             "tensorflow-metal",
             "tensorpack>=0.11",
             "tf_slim>=1.1.0",