v1.9

HenriquesLab · Aug 7, 2020 · 057412d · 057412d
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Showing 15 changed files with 14 additions and 12 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/Colab_notebooks/.DS_Store b/Colab_notebooks/.DS_Store
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
@@ -19,12 +19,14 @@ Main notebooks:
 ——————————————
 
 - StarDist 2D, StarDist 3D, CARE 2D and CARE 3D notebooks now uses TensorFlow 2.2 (instead of TF 1.5.15)
+
 - YOLOv2 notebook: QC section now uses the same mAP function as the training, for better consistency of results; ground-truth labels and predicted labels in the QC section are exported to the QC folder as csv files which holde the bounding box coordinates and class labels; Display of prediction results now more consistent with display of GT labels; Updated Augmentation Section, now between 2-8 times augmentation of dataset possible; Additional csv file with predicted bounding box coordinates in a format suitable for use in imageJ as Results Table is now exported to the user's results folder in the Prediction section; Added 'training_times' as hyperparameter for improved tuning of model training; Tracking of mAP during training implemented; After training, model with best validation performance, best mAP score and the last model weights are saved to allow easier performance comparison by the user; Updated explanation of parameters and QC section.
 
 - 3D U-Net:
     1. Added ability to train network on non-binary targets
     2. Added ability to choose loss, metrics and optimizer
     3. Fixed data generator bug leading to erroneous generator length when choosing random_crop
+    4. Added support for using the imgaug library and creating custom augmentation pipelines
 
 + minor modifications and bug fixes
 

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/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/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/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/fnet_ZeroCostDL4Mic.ipynb b/Colab_notebooks/fnet_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks/pix2pix_ZeroCostDL4Mic.ipynb b/Colab_notebooks/pix2pix_ZeroCostDL4Mic.ipynb