v1.10

HenriquesLab · Aug 15, 2020 · 28257e6 · 28257e6
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diff --git a/Colab_notebooks/Beta notebooks/DenoiSeg_2D_ZeroCostDL4Mic.ipynb b/Colab_notebooks/Beta notebooks/DenoiSeg_2D_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks/CARE_2D_ZeroCostDL4Mic.ipynb b/Colab_notebooks/CARE_2D_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks/CARE_3D_ZeroCostDL4Mic.ipynb b/Colab_notebooks/CARE_3D_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks/ChangeLog.txt b/Colab_notebooks/ChangeLog.txt
@@ -7,6 +7,28 @@ Latest releases available here:
 /~https://github.com/HenriquesLab/ZeroCostDL4Mic/releases
 
 
+—————————————————————————————————————————————————————————
+ZeroCostDL4Mic v1.10
+
+
+Major changes:
+
+- New beta notebook : DenoiSeg 2D
+
+- StarDist 2D, StarDist 3D, CARE 2D and CARE 3D notebooks now back to TensorFlow 1.5 (instead of TF 2.2, issues with TF 2.3)
+
+- Deep-STORM now runs on TensorFlow 2.3
+
+- Models trained using StarDist 2D, CARE 2D, CARE 3D, DenoiSeg 2D, Noise2Void 2D and 3D notebooks can be used in Fiji via their respective plugin
+
+
+—————————————————————————————————————————————————————————
+ZeroCostDL4Mic v1.9
+
+Minor aesthetic bug fixes (titles and section naming mostly).
+
+
+
 —————————————————————————————————————————————————————————
 ZeroCostDL4Mic v1.8
 

diff --git a/Colab_notebooks/CycleGAN_ZeroCostDL4Mic.ipynb b/Colab_notebooks/CycleGAN_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks/Deep-STORM_2D_ZeroCostDL4Mic.ipynb b/Colab_notebooks/Deep-STORM_2D_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks/LICENSE.txt b/Colab_notebooks/LICENSE.txt
diff --git a/Colab_notebooks/Noise2Void_2D_ZeroCostDL4Mic.ipynb b/Colab_notebooks/Noise2Void_2D_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks/Noise2Void_3D_ZeroCostDL4Mic.ipynb b/Colab_notebooks/Noise2Void_3D_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks/ReadMe.txt b/Colab_notebooks/ReadMe.txt
diff --git a/Colab_notebooks/StarDist_2D_ZeroCostDL4Mic.ipynb b/Colab_notebooks/StarDist_2D_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks/StarDist_3D_ZeroCostDL4Mic.ipynb b/Colab_notebooks/StarDist_3D_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks/Template_ZeroCostDL4Mic.ipynb b/Colab_notebooks/Template_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks/U-Net_3D_ZeroCostDL4Mic.ipynb b/Colab_notebooks/U-Net_3D_ZeroCostDL4Mic.ipynb
@@ -53,7 +53,7 @@
         "\n",
         "<font size = 4>[**3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation**](https://arxiv.org/pdf/1606.06650.pdf) by Özgün Çiçek *et al.* published on arXiv in 2016\n",
         "\n",
-        "<font size = 4>The following three Python libraries play an important role in the notebook: \n",
+        "<font size = 4>The following two Python libraries play an important role in the notebook: \n",
         "\n",
         "1. <font size = 4>[**Elasticdeform**](/~https://github.com/gvtulder/elasticdeform)\n",
         " by Gijs van Tulder was used to augment the 3D training data using elastic grid-based deformations as described in the original 3D U-Net paper. \n",
@@ -1302,21 +1302,21 @@
         "\n",
         "#@markdown ###Data augmentation\n",
         "\n",
-        "apply_data_augmentation = False #@param {type:\"boolean\"}\n",
+        "apply_data_augmentation = True #@param {type:\"boolean\"}\n",
         "\n",
         "# List of augmentations\n",
         "augmentations = []\n",
         "\n",
         "#@markdown ###Gaussian blur\n",
-        "add_gaussian_blur = False #@param {type:\"boolean\"}\n",
+        "add_gaussian_blur = True #@param {type:\"boolean\"}\n",
         "gaussian_sigma =   0.7#@param {type:\"number\"}\n",
         "gaussian_frequency = 0.5 #@param {type:\"number\"}\n",
         "\n",
         "if add_gaussian_blur:\n",
         "    augmentations.append(iaa.Sometimes(gaussian_frequency, iaa.GaussianBlur(sigma=(0, gaussian_sigma))))\n",
         "\n",
         "#@markdown ###Linear contrast\n",
-        "add_linear_contrast = False #@param {type:\"boolean\"}\n",
+        "add_linear_contrast = True #@param {type:\"boolean\"}\n",
         "contrast_min =  0.4 #@param {type:\"number\"}\n",
         "contrast_max =   1.6#@param {type:\"number\"}\n",
         "contrast_frequency = 0.5 #@param {type:\"number\"}\n",
@@ -1335,24 +1335,22 @@
         "\n",
         "#@markdown ###Add custom augmenters\n",
         "\n",
-        "augmenters = \"\" #@param {type:\"string\"}\n",
+        "augmenters = \"GammaContrast; AverageBlur; LinearContrast\" #@param {type:\"string\"}\n",
         "\n",
-        "augmenter_params = \"\" #@param {type:\"string\"}\n",
+        "augmenter_params = \"(0.5, 2.0); (0.5, 2.0); (0.4, 1.6)\" #@param {type:\"string\"}\n",
         "\n",
-        "augmenter_frequency = \"\" #@param {type:\"string\"}\n",
+        "augmenter_frequency = \"0.3; 0.4; 0.5\" #@param {type:\"string\"}\n",
         "\n",
-        "if len(augmenters) > 0 and len(augmenter_params) > 0 and len(augmenter_frequency) > 0:\n",
-        "    aug_lst = augmenters.split(';')\n",
-        "    aug_params_lst = augmenter_params.split(';')\n",
-        "    aug_freq_lst = augmenter_frequency.split(';')\n",
+        "aug_lst = augmenters.split(';')\n",
+        "aug_params_lst = augmenter_params.split(';')\n",
+        "aug_freq_lst = augmenter_frequency.split(';')\n",
         "\n",
-        "    assert len(aug_lst) == len(aug_params_lst) and len(aug_lst) == len(aug_freq_lst), 'The number of arguments in augmenters, augmenter_params and augmenter_frequency are not the same!'\n",
+        "assert len(aug_lst) == len(aug_params_lst) and len(aug_lst) == len(aug_freq_lst), 'The number of arguments in augmenters, augmenter_params and augmenter_frequency are not the same!'\n",
         "\n",
-        "    for __, (aug, param, freq) in enumerate(zip(aug_lst, aug_params_lst, aug_freq_lst)):\n",
-        "        aug, param, freq = aug.strip(), param.strip(), freq.strip() \n",
-        "        aug_func = iaa.Sometimes(eval(freq), getattr(iaa, aug)(eval(param)))\n",
-        "        if apply_data_augmentation:\n",
-        "            augmentations.append(aug_func)\n",
+        "for __, (aug, param, freq) in enumerate(zip(aug_lst, aug_params_lst, aug_freq_lst)):\n",
+        "    aug, param, freq = aug.strip(), param.strip(), freq.strip() \n",
+        "    aug_func = iaa.Sometimes(eval(freq), getattr(iaa, aug)(eval(param)))\n",
+        "    augmentations.append(aug_func)\n",
         "\n",
         "#@markdown ###Elastic deformations\n",
         "add_elastic_deform = True #@param {type:\"boolean\"}\n",
@@ -1388,10 +1386,7 @@
         "                                       downscale=downscaling_in_xy,\n",
         "                                       binary_target=binary_target)\n",
         "\n",
-        "if apply_data_augmentation:\n",
-        "    sample_src_aug, sample_tgt_aug = train_generator.sample_augmentation(random.randint(0, len(train_generator)))\n",
-        "else:\n",
-        "    sample_src_aug, sample_tgt_aug = train_generator.__getitem__(random.randint(0, len(train_generator)))\n",
+        "sample_src_aug, sample_tgt_aug = train_generator.sample_augmentation(random.randint(0, len(train_generator)))\n",
         "\n",
         "def scroll_in_z(z):\n",
         "    f=plt.figure(figsize=(16,8))\n",
@@ -1499,8 +1494,8 @@
       "metadata": {
         "id": "y_DtHgr-41K0",
         "colab_type": "code",
-        "cellView": "form",
-        "colab": {}
+        "colab": {},
+        "cellView": "form"
       },
       "source": [
         "#@markdown ##Download model directory\n",
@@ -1510,7 +1505,7 @@
         "\n",
         "from google.colab import files\n",
         "\n",
-        "model_path_download = \"\" #@param {type:\"string\"}\n",
+        "model_path_download = \"/content/gdrive/My Drive/Crick/ZeroCostDL4Mic/Eva Masters Project/test_newest_notebook_run1\" #@param {type:\"string\"}\n",
         "\n",
         "if len(model_path_download) == 0:\n",
         "    model_path_download = full_model_path\n",
@@ -1550,7 +1545,11 @@
         "cellView": "form",
         "colab_type": "code",
         "id": "EdcnkCr9Nbl8",
-        "colab": {}
+        "colab": {
+          "base_uri": "https://localhost:8080/",
+          "height": 34
+        },
+        "outputId": "1088857c-2d43-4018-95dd-77f4ca24a576"
       },
       "source": [
         "#@markdown ###Model to be evaluated:\n",
@@ -1574,7 +1573,15 @@
         "    print('Please make sure you provide a valid model path and model name before proceeding further.')\n"
       ],
       "execution_count": null,
-      "outputs": []
+      "outputs": [
+        {
+          "output_type": "stream",
+          "text": [
+            "test_newest_notebook_run1 will be evaluated\n"
+          ],
+          "name": "stdout"
+        }
+      ]
     },
     {
       "cell_type": "markdown",
@@ -1939,7 +1946,7 @@
         "\n",
         "# Tifffile library issues means that images cannot be appended to \n",
         "#@markdown <font size = 3>Choose if prediction file exceeds 4GB or if input file is very large (above 2GB). Image volume saved as BigTIFF.\n",
-        "big_tiff = False #@param {type:\"boolean\"}\n",
+        "big_tiff = True #@param {type:\"boolean\"}\n",
         "\n",
         "#@markdown <font size = 3>Reduce `prediction_depth` if runtime runs out of memory during prediction. Only relevant if prediction saved as BigTIFF\n",
         "\n",

diff --git a/Colab_notebooks/U-net_2D_ZeroCostDL4Mic.ipynb b/Colab_notebooks/U-net_2D_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks/YOLOv2_ZeroCostDL4Mic.ipynb b/Colab_notebooks/YOLOv2_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks/ZeroCostDL4Mic_UserManual_v1.2.pdf b/Colab_notebooks/ZeroCostDL4Mic_UserManual_v1.2.pdf
diff --git a/Colab_notebooks/fnet_ZeroCostDL4Mic.ipynb b/Colab_notebooks/fnet_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks/pix2pix_ZeroCostDL4Mic.ipynb b/Colab_notebooks/pix2pix_ZeroCostDL4Mic.ipynb