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HenriquesLab / ZeroCostDL4Mic

ZeroCostDL4Mic: A Google Colab based no-cost toolbox to explore Deep-Learning in Microscopy
MIT License
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Issue saving simulated data in Deep-STORM notebook. #311

Open dickinson-lab opened 6 months ago

dickinson-lab commented 6 months ago

Describe the bug I am using the DeepSTORM colab notebook to train a network using simulated images. Cell 3.1b.2 should save the simulated images at TIFs, but it doesn't appear to work. It does not give an error, but does not write any image files.

To Reproduce Steps to reproduce the behavior:

  1. Go to https://colab.research.google.com/github/HenriquesLab/ZeroCostDL4Mic/blob/master/Colab_notebooks/Deep-STORM_2D_ZeroCostDL4Mic.ipynb
  2. Run steps 1, 2 and the first step of 3.1b (simulating data).
  3. Enter a path and run the cell labeled "Play this cell to save the simulated stack." I have tested both local paths (/Volumes/myName/path/to/mydirectory) and drive paths (drive/myDeepSTORMfolder).
  4. The message displayed is "Folder created. Training dataset saved." But no folder is created and no TIFF files are saved in the specified locations.
  5. Run the same cell again. Now the message displayed is "Training data already exists in folder: Data overwritten. Training dataset saved." But there are still no TIFF files in the specified location.

Expected behavior There should be 20 new TIFF files in the specified folder, corresponding to simulated training data.