We provide a set of demo notebooks to get started with using CEBRA. To run the notebooks, you need a working Jupyter notebook server, a CEBRA installation, and the datasets required to run the notebooks, available on FigShare.

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   Encoding of space, hippocampus (CA1) <demo_notebooks/Demo_hippocampus.ipynb>
   Decoding movie features from (V1) visual cortex <demo_notebooks/Demo_Allen.ipynb>
   Forelimb dynamics, somatosensory (S1) <demo_notebooks/Demo_primate_reaching.ipynb>
   Synthetic neural benchmarking <demo_notebooks/Demo_synthetic_exp.ipynb>
   Hypothesis-driven analysis <demo_notebooks/Demo_hypothesis_testing.ipynb>
   Consistency <demo_notebooks/Demo_consistency.ipynb>
   Decoding <demo_notebooks/Demo_decoding.ipynb>
   Topological data analysis <demo_notebooks/Demo_cohomology.ipynb>
   Technical: Training models across animals <demo_notebooks/Demo_hippocampus_multisession.ipynb>
   Technical: conv-piVAE <demo_notebooks/Demo_conv-pivae.ipynb>
   Technical: S1 training with MSE loss <demo_notebooks/Demo_primate_reaching_mse_loss.ipynb>
   Technical: Learning the temperature parameter <demo_notebooks/Demo_learnable_temperature.ipynb>

The demo notebooks can also be found in the demo_notebooks/ subdirectory in the CEBRA repository.

Before you can run these notebooks, you must have a working installation of CEBRA. Please see the dedicated :doc:`Installation Guide </installation>` for information on installation options using conda, pip and docker.

Synthetic Experiment Demo (CEBRA, piVAE, tSNE, UMAP): This demo requires several additional packages that have differing requirements to CEBRA. Therefore, we recommend using the supplied docker container or conda cebra-full env.

We host prepackaged data on figshare. Please download them and check the loading directory is correct in the notebook. By default we assume you have downloaded the data in the ./data/ directory in the repository root.

For different paths, you can specify the CEBRA_DATADIR=... environment variable. You can do this by placing import os; os.environ['CEBRA_DATADIR'] = "path/to/your/data" at the top of your notebook.

For reference, the original data is available at:

• Hippocampus dataset, using a preprocessing script.
• Primate S1 dataset.
• Allen Institute Neuropixels dataset and 2P dataset.