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 works best if the machine you are working on has Jupyter notebook installed such that double-clicking opens it. One recommended way:

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

Trigger feature

There are 2 ways to start that 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 (requires ScopeFoundry 2.0+ see getting started tutorial)

cd "to/your_data_folder"
conda activate scopefoundry 
# or for mac: 
# source activate scopefoundry
python -m ScopeFoundry.tools

​ and clicking the corresponding button on the Welcome tap.

In that folder the feature generates

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

analyze_with_ipynb

In the notebook the top 2 cells are generated:

In cell 1: imports of data loaders

In cell 2: lists path to each .h5 file and how it could be loaded