_toc.yml

format: jb-book
root: index

parts:
  - caption: Labs
    chapters:
    - file: labs/00_pytorch_primer.ipynb
    - file: labs/01_spike_sorting.ipynb
    - file: labs/02_calcium_imaging.ipynb
    - file: labs/03_pose_tracking.ipynb
    - file: labs/04_glms.ipynb
    - file: labs/05_decoding.ipynb
    - file: labs/06_arhmm.ipynb
    - file: labs/07_slds.ipynb
    - file: labs/08_lfads.ipynb

  - caption: Foundations
    chapters:
    - file: lectures/02_probabilistic_modeling.ipynb
    - file: lectures/03_neurobio.ipynb

  - caption: "Unit I: Signal Extraction"
    chapters:
    - file: lectures/04_simple_spike_sorting.ipynb
    - file: lectures/05_deconv_spike_sorting.ipynb
    - file: lectures/06_calcium_imaging.ipynb
    - file: lectures/07_pose_tracking.ipynb

  - caption: "Unit II: Encoding & Decoding"
    chapters:
    - file: lectures/08_summary_stats.ipynb
    - file: lectures/09_glm.ipynb
    - file: lectures/10_poisson_processes.ipynb
    - file: lectures/11_decoding.ipynb

  - caption: "Unit III: Unsupervised Learning"
    chapters:
    - file: lectures/12_mixtures_em.ipynb
    - file: lectures/13_hmms.md
    - file: lectures/poldrack_fmri_analysis.ipynb

  - caption: References
    chapters:
    - file: lectures/99_references.md