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bioimageloader
bioimageloader

Contents

  • Installation
  • User Guides
    • Basic: Prepare datasets
    • Basic: Basic usage
    • Basic: Load multiple datasets
    • Basic: Deep learning with PyTorch
    • More: Split training/test set
    • More: Speeding up loading by pre-parsing
    • More: Modifying existing collections
    • More: Writing a custom Dataset
  • Notebooks
    • ML: Data statistics with PCA
    • DL: Deep learning with BioImage.IO
    • DL: StarDist and Cellpose
    • DL: Training Stardist and Cellpose Models
    • (tmp) Setup
    • DL: Benchmark Table
  • Collection Catalogue
  • Miscellaneous
    • TensorFlow installation
    • PyTorch installation
  • API
    • bioimageloader
    • bioimageloader.base
    • bioimageloader.common
    • bioimageloader.collections
    • bioimageloader.batch
    • bioimageloader.utils
    • bioimageloader.transforms
  • Contributing
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Notebooks#

We all love jupyter notebooks. Here are some notebooks!

All notebooks are available under notebooks directory in the git repository.

Jupyter notebooks

  • ML: Data statistics with PCA
  • DL: Deep learning with BioImage.IO
  • DL: StarDist and Cellpose
  • DL: Training Stardist and Cellpose Models
  • (tmp) Setup
  • DL: Benchmark Table
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ML: Data statistics with PCA
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More: Writing a custom Dataset
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