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.

This feature works best with Jupyter Notebook installed. We recommend:

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

There are two ways to start this feature:

In app:

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

Without app:

Using ScopeFoundry tools (install instructions here):

cd "to/your_folder_with_data"

Potentially (conda activate scopefoundry):

python -m ScopeFoundry.tools

Then click the button on the Welcome tab.

Result

This feature generates:

  1. An h5_data_loaders.py file containing convenience methods based on the contents in the .h5 files.
  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.