Analyze with ipynb

Given a folder with .h5 files, use this feature to analyze data quickly. It provides convenient loading functions and an overview Jupyter notebook.

Recommendation

This feature requires Jupyter Notebook to be installed. It works best when launching an .ipynb file (e.g., by double-clicking) opens a Jupyter editor. One recommended way:

  1. Install Visual Studio Code.
  2. Install extensions:
    1. Pylance (Microsoft)
    2. Jupyter (Microsoft)

Trigger feature

There are two ways to start this feature:

  1. From ScopeFoundry: Advanced -> Analyze with ipynb. The folder acted upon is the one defined in the app/save_dir settings (bottom left panel).

    Screenshot 2025-01-12 at 17.45.20

  2. Using ScopeFoundry tools (install instructions here):

    cd "to/your_folder_with_data"

    Potentially (conda activate scopefoundry):

    python -m ScopeFoundry.tools

    Then click the corresponding button on the Welcome tab.

Benefit

This feature generates:

  1. An h5_data_loaders.py file containing convenience methods based on the .h5 file content.
  2. An overview.ipynb file where you can start your analysis.

analyze_with_ipynb

In the notebook, the top two cells are generated:

  • Cell 1: Imports of data loaders.
  • Cell 2: Lists paths to each .h5 file and how it can be loaded.