https://github.com/neuronets/nobrainer-book
Tutorial and guides for the Nobrainer framework
https://github.com/neuronets/nobrainer-book
Last synced: 3 months ago
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Tutorial and guides for the Nobrainer framework
- Host: GitHub
- URL: https://github.com/neuronets/nobrainer-book
- Owner: neuronets
- Created: 2022-08-27T01:14:26.000Z (almost 4 years ago)
- Default Branch: master
- Last Pushed: 2024-07-18T12:51:46.000Z (almost 2 years ago)
- Last Synced: 2025-01-07T17:19:27.232Z (over 1 year ago)
- Homepage: http://neuronets.dev/nobrainer-book/
- Size: 3.52 MB
- Stars: 0
- Watchers: 3
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
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README
# Nobrainer Book
Tutorials and guides for [Nobrainer](https://github.com/neuronets/nobrainer) —
a deep learning framework for 3D brain image processing.
## Tutorials
Follow these tutorials in order for a complete learning journey:
| # | Tutorial | What you'll learn |
|---|----------|-------------------|
| 01 | Getting Started | Install, import, explore available models |
| 02 | Download & Inspect | Get sample brain MRI data, understand NIfTI format |
| 03 | Extract & Batch | Prepare training data with patches and datasets |
| 04 | Brain Segmentation | Train a UNet in 3 lines with the estimator API |
| 05 | Uncertainty | Bayesian inference with variance and entropy maps |
| 06 | Brain Generation | Synthesize brain volumes with Progressive GAN |
| 07 | Advanced Training | Custom PyTorch loops for full control |
| 08 | Model Management | Save/load with Croissant-ML metadata |
| 09 | Zarr Pipeline | Cloud-optimized multi-resolution storage |
| 10 | Multi-GPU | Scale training across GPUs with DDP |
| 11 | Contributing | Add models, write tests, submit PRs |
## Run in Google Colab
**Stable release** (master):
[](https://colab.research.google.com/github/neuronets/nobrainer-book/blob/master)
**Pre-release** (alpha):
[](https://colab.research.google.com/github/neuronets/nobrainer-book/blob/alpha)
## Branches
| Branch | Nobrainer version | Install |
|--------|-------------------|---------|
| master | Stable | `pip install nobrainer` |
| alpha | Pre-release | `pip install --pre nobrainer` |
## Run locally
```bash
uv venv --python 3.14
source .venv/bin/activate
uv pip install "nobrainer[bayesian,generative,zarr]" monai pyro-ppl nilearn matplotlib
for script in docs/nobrainer-guides/scripts/[01]*.py; do python "$script"; done
```