v1.8

Shift of beta notebooks as main release
HenriquesLab · Aug 5, 2020 · e38c828 · e38c828
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diff --git a/.DS_Store b/.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
@@ -6,6 +6,29 @@ https://www.biorxiv.org/content/10.1101/2020.03.20.000133v1
 Latest releases available here:
 https://github.com/HenriquesLab/ZeroCostDL4Mic/releases
 
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+—————————————————————————————————————————————————————————
+ZeroCostDL4Mic v1.8
+
+Major changes:
+
+- Beta Notebooks have now been move to main notebooks
+- The StarDist 2D Fiji notebook is now obselete as the model export works in the main notebook.
+
+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
+
++ minor modifications and bug fixes
+
+
 —————————————————————————————————————————————————————————
 ZeroCostDL4Mic v1.7
 

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/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
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/ZeroCostDL4Mic_UserManual_v1.pdf b/Colab_notebooks/ZeroCostDL4Mic_UserManual_v1.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
diff --git a/Colab_notebooks_Beta/CycleGAN_ZeroCostDL4Mic.ipynb b/Colab_notebooks_Beta/CycleGAN_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks_Beta/DeepSTORM_2D_ZeroCostDL4Mic.ipynb b/Colab_notebooks_Beta/DeepSTORM_2D_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks_Beta/Stardist_2D_Fiji_ZeroCostDL4Mic.ipynb b/Colab_notebooks_Beta/Stardist_2D_Fiji_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks_Beta/U-net_3D_ZeroCostDL4Mic.ipynb b/Colab_notebooks_Beta/U-net_3D_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks_Beta/YoloV2_ZeroCostDL4Mic.ipynb b/Colab_notebooks_Beta/YoloV2_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks_Beta/pix2pix_ZeroCostDL4Mic.ipynb b/Colab_notebooks_Beta/pix2pix_ZeroCostDL4Mic.ipynb