Upload for v1.13 release

HenriquesLab · Jul 2, 2021 · 4d8f690 · 4d8f690
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diff --git a/Colab_notebooks/Beta notebooks/3D-RCAN_ZeroCostDL4Mic.ipynb b/Colab_notebooks/Beta notebooks/3D-RCAN_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks/Beta notebooks/Cellpose_2D_ZeroCostDL4Mic.ipynb b/Colab_notebooks/Beta notebooks/Cellpose_2D_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks/Beta notebooks/DRMIME_2D_ZeroCostDL4Mic.ipynb b/Colab_notebooks/Beta notebooks/DRMIME_2D_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks/Beta notebooks/DecoNoising_2D_ZeroCostDL4Mic.ipynb b/Colab_notebooks/Beta notebooks/DecoNoising_2D_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks/Beta notebooks/Deep-STORM_2D_ZeroCostDL4Mic_BioImageModelZoo_export.ipynb b/Colab_notebooks/Beta notebooks/Deep-STORM_2D_ZeroCostDL4Mic_BioImageModelZoo_export.ipynb
diff --git a/Colab_notebooks/Beta notebooks/DenoiSeg_ZeroCostDL4Mic.ipynb b/Colab_notebooks/Beta notebooks/DenoiSeg_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks/Beta notebooks/Detectron2_2D_ZeroCostDL4Mic.ipynb b/Colab_notebooks/Beta notebooks/Detectron2_2D_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks/Beta notebooks/MaskRCNN_ZeroCostDL4Mic.ipynb b/Colab_notebooks/Beta notebooks/MaskRCNN_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks/Beta notebooks/U-Net_2D_ZeroCostDL4Mic_BioImageModelZoo_export.ipynb b/Colab_notebooks/Beta notebooks/U-Net_2D_ZeroCostDL4Mic_BioImageModelZoo_export.ipynb
diff --git a/Colab_notebooks/Beta notebooks/U-Net_3D_ZeroCostDL4Mic_BioImageModelZoo_export.ipynb b/Colab_notebooks/Beta notebooks/U-Net_3D_ZeroCostDL4Mic_BioImageModelZoo_export.ipynb
diff --git a/Colab_notebooks/Beta notebooks/ZeroCostDL4Mic_Interactive_annotations_Cellpose.ipynb b/Colab_notebooks/Beta notebooks/ZeroCostDL4Mic_Interactive_annotations_Cellpose.ipynb
diff --git a/Colab_notebooks/Beta notebooks/fnet_2D_ZeroCostDL4Mic.ipynb b/Colab_notebooks/Beta notebooks/fnet_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 @@ https://www.biorxiv.org/content/10.1101/2020.03.20.000133v4
 Latest releases available here:
 /~https://github.com/HenriquesLab/ZeroCostDL4Mic/releases
 
+—————————————————————————————————————————————————————————
+ZeroCostDL4Mic v1.13
+
+Major changes:
+- added a new export of requirements.txt file with minimal packages, better compatibility with local runtime sessions
+- Beta notebooks: new notebooks available: Detectron2 (object detection), MaskRCNN (object detection and segmentation), DRMIME (image registration), Cellpose (image segmentation) (2D) and DecoNoising (denoising) (2D).
+- Addition of the Interactive segmentation - Cellpose notebook, using Kaibu and ImJoy, big thanks to Wei Ouyang for helping us get this up and running. 
+- Tools: A notebook to perform Quality Control has been added
+- Noise2Void 2D and 3D now use the latest code release based on TensorFlow 2
+- The version check is now done on a per-notebook basis, making release of individual notebooks easier.
+- U-Net 3D imports Keras libraries via TensorFlow.
+- Section 1 and 2 in the notebooks have been swapped for a better flow and improved capabilities for export of requirements.txt
+- Each notebook now includes a version log, that will be individually amended when doing individual notebook releases.
+- Fnet: A 2D notebook was added, the fnet notebooks have an additional cell that creates the data files, Fnet 3D's re-training cell now   has a module to reduce images in the buffer, just as the main training cell (to avoid OOM error).
+- YOLOv2: The repository is now saved in the content folder of colab rather than the users gdrive, consistent with other notebooks , Commented code was removed.
+
++ minor bug fixes
+
+Beta notebooks:
+- model export to BioImage Model Zoo format for DeepImageJ for 2D U-Net, 3D U-Net and Deep-STORM
+- Cellpose notebook now exports PDF during training and QC. Cellpose now trains using Torch. The new Cyto2 model is also available.
+
 
 —————————————————————————————————————————————————————————
 ZeroCostDL4Mic v1.12

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/Latest_ZeroCostDL4Mic_Release.csv b/Colab_notebooks/Latest_ZeroCostDL4Mic_Release.csv
@@ -1 +1 @@
-1.12
+1.13
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_2D_ZeroCostDL4Mic.ipynb b/Colab_notebooks/U-Net_2D_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/YOLOv2_ZeroCostDL4Mic.ipynb b/Colab_notebooks/YOLOv2_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks/fnet_2D_ZeroCostDL4Mic.ipynb b/Colab_notebooks/fnet_2D_ZeroCostDL4Mic.ipynb
diff --git a/Colab_notebooks/fnet_3D_ZeroCostDL4Mic.ipynb b/Colab_notebooks/fnet_3D_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