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README.md

FlyWire connectome analysis tutorial

Local setup (Linux/macOS/Windows):

  1. Clone this repository.
  2. Install the Pixi package manager.
  3. Run pixi install in the connectomics_tutorial directory.
  4. Point your notebook editor of choice to the Python interpreter installed in the .pixi directory and open tutorial.ipynb.

If you don't have a notebook editor installed, you can run

pixi run jupyter notebook tutorial.ipynb

to open the tutorial in the Jupyter editor.

Paperspace Gradient setup (Ubuntu 22.04 runtime, the default as of July 2025):

Just clone this repository, and then tutorial.ipynb should be ready to run.

Colab setup (Ubuntu 22.04 runtime, the default as of July 2025):

Just open tutorial.ipynb in Colab and it should be ready to run.