_toc.yml

# Table of contents
# Learn more at https://jupyterbook.org/customize/toc.html

format: jb-book
root: intro

parts:
  - caption: Brain Building Blocks
    chapters:
    - file: Fundamentals/BrainBuildingBlocks/Session1/S1_Intro
      sections:
        - file: Fundamentals/BrainBuildingBlocks/Session1/S1L1_HelloBrain
        - file: Fundamentals/BrainBuildingBlocks/Session1/S1L2_EssentialNeuroanatomy
        - file: Fundamentals/BrainBuildingBlocks/Session1/S1L3_FunctionalAreaAndNetwork
        - file: Fundamentals/BrainBuildingBlocks/Session1/S1L4_LanguageOfTheBrain
    - file: Fundamentals/BrainBuildingBlocks/Session2/S2_Intro
      sections:
        - file: Fundamentals/BrainBuildingBlocks/Session2/S2L1_IntroBrainScienceToolbox
        - file: Fundamentals/BrainBuildingBlocks/Session2/S2L2_EraOfLocalization
        - file: Fundamentals/BrainBuildingBlocks/Session2/S2L3_MeasuringImmeasurable
        - file: Fundamentals/BrainBuildingBlocks/Session2/S2L4_SneakPeekInsideTheBlackBox
        - file: Fundamentals/BrainBuildingBlocks/Session2/S2L5_JourneyIntoTheBrain
    - file: Fundamentals/BrainBuildingBlocks/Session3/S3_Intro
      sections:
        - file: Fundamentals/BrainBuildingBlocks/Session3/S3L1_ConnectingBrainAndBehavior
        - file: Fundamentals/BrainBuildingBlocks/Session3/S3L2_SingleNeuronStudies
        - file: Fundamentals/BrainBuildingBlocks/Session3/S3L3_EEGStudies
        - file: Fundamentals/BrainBuildingBlocks/Session3/S3L4_fMRIStudies
    - file: Fundamentals/BrainBuildingBlocks/Session4/S4_Intro
      sections:
        - file: Fundamentals/BrainBuildingBlocks/Session4/S4L1_SolveTheBrainSignal
        - file: Fundamentals/BrainBuildingBlocks/Session4/S4L2_NeuralFiring
        - file: Fundamentals/BrainBuildingBlocks/Session4/S4L3_EEGSignal
        - file: Fundamentals/BrainBuildingBlocks/Session4/S4L4_fMRISignal

    - file: Fundamentals/BrainBuildingBlocks/Session5/S5_Intro
      sections:
        - file: Fundamentals/BrainBuildingBlocks/Session5/S5L1_TopographicOrganization
        - file: Fundamentals/BrainBuildingBlocks/Session5/S5L2_BiologicalNeuron
        - file: Fundamentals/BrainBuildingBlocks/Session5/S5L3_NeuralPopulationTuning
        - file: Fundamentals/BrainBuildingBlocks/Session5/S5L4_NeuralRepresentation
    - file: Fundamentals/BrainBuildingBlocks/Session6/S6_Intro
      sections:
        - file: Fundamentals/BrainBuildingBlocks/Session6/S6L1_DataHandlingAndExploration
        - file: Fundamentals/BrainBuildingBlocks/Session6/S6L2_GoalsOfModeling
        - file: Fundamentals/BrainBuildingBlocks/Session6/S6L3_TypesOfModeling
        - file: Fundamentals/BrainBuildingBlocks/Session6/S6L4_ModelEvaluation
    - file: Fundamentals/BrainBuildingBlocks/Session7/S7_Intro
      sections:
        - file: Fundamentals/BrainBuildingBlocks/Session7/S7L1_AIAndBI
        - file: Fundamentals/BrainBuildingBlocks/Session7/S7L2_AIAndBI2
        - file: Fundamentals/BrainBuildingBlocks/Session7/S7L3_SupervisedDeepLearning
        - file: Fundamentals/BrainBuildingBlocks/Session7/S7L4_ReinforcementLearning
        - file: Fundamentals/BrainBuildingBlocks/Session7/S7L5_UnsupervisedLearning
        - file: Fundamentals/BrainBuildingBlocks/Session7/S7L6_LanguageModels
    - file: Fundamentals/BrainBuildingBlocks/Session8/S8_Intro
      sections:
      - file: Fundamentals/BrainBuildingBlocks/Session8/S8L1_DiagnosisAndMonitoring
      - file: Fundamentals/BrainBuildingBlocks/Session8/S8L4_ComputationalNeuropsychiatry
    - file: Fundamentals/BrainBuildingBlocks/Session9/S9_Intro
      sections:
      - file: Fundamentals/BrainBuildingBlocks/Session9/S9L2_BrainComputerInterface
  - caption: Prerequisites
    chapters:
    - file: Fundamentals/Prereqs/00_basic_python
      title: Python
    - file: Fundamentals/Prereqs/01_numpy
      title: Numpy

  - caption: Welcome to Brain Code Camp! (Week 1)
    chapters:
    - file: Fundamentals/WelcomeToBrainCodeCamp/Intro

  - caption: Computational Neuroscience (Week 2)
    chapters:
    - file: Fundamentals/ComputationalNeuroscience/Intro

  - caption: Intro to Modeling and Model Selection (Week 3)
    chapters:
    - file: Fundamentals/IntroToModeling/modeling_intro
    - file: Fundamentals/IntroToModeling/modeling_part1_simple_linear_model
    - file: Fundamentals/IntroToModeling/modeling_part2_poly_overfit_regularization
    - file: Fundamentals/IntroToModeling/modeling_part3_data_splitting
    - file: Fundamentals/IntroToModeling/modeling_outro
  
  - caption: Dimensionality Reduction (Week 4)
    chapters:
    - file: Fundamentals/DimensionalityReduction/dim_reduct_intro
    - file: Fundamentals/DimensionalityReduction/dim_reduct_part1_basics
    - file: Fundamentals/DimensionalityReduction/dim_reduct_part2_pca
    - file: Fundamentals/DimensionalityReduction/dim_reduct_part3_pca_CDT_images
    - file: Fundamentals/DimensionalityReduction/dim_reduct_part4_nonlinear_methods
    - file: Fundamentals/DimensionalityReduction/dim_reduct_outro

  - caption: Machine Learning (Weeks 5-6)
    chapters:
    - file: Fundamentals/MachineLearning/ml_part1_intro
      title: ML Part 1 (Week 5)
      sections:
      - file: Fundamentals/MachineLearning/intro_to_machine_learning
        title: Introduction to Machine Learning
      - file: Fundamentals/MachineLearning/logistic_regression
        title: Logistic Regression
      - file: Fundamentals/MachineLearning/svm
        title: Support Vector Machines
    - file: Fundamentals/MachineLearning/ml_part2_intro
      title: ML Part 2 (Week 6)
      sections: 
      - file: Fundamentals/MachineLearning/decision_tree_random_forest
        title: Decision Trees and Random Forest
      - file: Fundamentals/MachineLearning/knn     
        title: K-Nearest Neighbors
      - file: Fundamentals/MachineLearning/eeg_supervised_learning
        title: EEG Analysis
      - file: Fundamentals/MachineLearning/ml_part2_outro

  - caption: Deep Learning (Week 7)
    chapters: 
    - file: Fundamentals/DeepLearning/deep_learning_intro
    - file: Fundamentals/DeepLearning/intro_pytorch
      title: Pytorch
    - file: Fundamentals/DeepLearning/intro_to_convolutional_nn
      title: CNN
    - file: Fundamentals/DeepLearning/thai_food_classification_transformers
      title: Image Classification
    - file: Fundamentals/DeepLearning/object_detection_transformer
      title: Object Detection
    - file: Fundamentals/DeepLearning/breast_cancer_segmentation_transformers
      title: Image Segmentation
    - file: Fundamentals/DeepLearning/deep_learning_outro

  - caption: Signal Processing (Week 8)
    chapters:
    - file: Fundamentals/SignalProcessing/signal_processing_intro
    - file: Fundamentals/SignalProcessing/signal_processing_part1_sampling_averaging
    - file: Fundamentals/SignalProcessing/signal_processing_part2_dft
    - file: Fundamentals/SignalProcessing/signal_processing_part3_STFT
    - file: Fundamentals/SignalProcessing/signal_processing_part4_application
    - file: Fundamentals/SignalProcessing/signal_processing_outro
    
  - caption: Applications (Weeks 9-11)
    chapters: 
    - file: Applications/EEG/EEG_Intro
      title: EEG (Week 9)
      sections:
      - file: Applications/EEG/motor_imagery_part1
      - file: Applications/EEG/motor_imagery_part2   
    - file: Applications/NeuralSpiking/Intro
      title: Neural Spiking (Week 10)
    - file: Applications/fMRI/Intro
      title: fMRI (Week 11)