### Biological Basis of the Code This script is part of a computational neuroscience model aimed at simulating and visualizing the spiking activities of different cellular components within the thalamic network under various oscillatory states. The biological relevance of the model focuses on the roles of specific neuron types within the thalamus and the dynamics associated with distinct brain oscillations. #### Key Biological Components 1. **Thalamic Network:** - The thalamus is a crucial brain structure involved in sensory signal relay, consciousness, and sleep regulation. It plays a significant role in generating brain oscillations like delta, spindle, alpha, and gamma waves. The code attempts to capture the spiking activity of thalamic neurons during these oscillations. 2. **Neuronal Population:** - Different types of thalamic neurons are modeled: - **TC (Thalamocortical) Cells:** These neurons have been divided into two groups in the code, TC1 and TC2, with distinct grid arrangements. They are integral in relaying sensory information from the thalamus to the cortex and are active participants in generating rhythmic oscillations. - **IN (Interneurons):** These primarily GABAergic neurons mediate inhibitory signals, contributing to the shaping of rhythmic activity and synchronization within the thalamic networks. - **RE (Reticular) Cells:** These neurons form the thalamic reticular nucleus, which plays a pivotal role in modulating the activity of thalamocortical cells through inhibitory connections and is involved in the generation of sleep spindles and other oscillations. #### Oscillation States 1. **Delta Oscillations:** - Predominantly observed during deep sleep, delta waves involve slow rhythms generated by the interplay between thalamocortical cells and thalamic reticular nucleus neurons. 2. **Spindle Waves:** - These are bursts of activity in the 7-14 Hz range, primarily occurring during non-REM sleep stages. RE cells prominently regulate and generate spindle oscillations through synchronized bursting. 3. **Alpha Oscillations:** - These are typically associated with relaxed states while awake, involving an interplay between thalamic and cortical activities. 4. **Gamma Oscillations:** - Higher oscillatory rhythms in the 30-100 Hz range, thought to be involved in sensory perception and cognitive processes. #### Script Functionality and Biological Modeling - **Raster Plot Generation:** - Spiking activities of different neuron types are visualized, allowing insight into the temporal patterns and frequency of firing in the network. - **Firing Rate Calculation:** - By evaluating the number of spikes within specific time frames, the script calculates mean firing rates for each type of thalamic neuron, reflecting their contribution to each oscillatory state. - **Temporal Dynamics:** - Different time windows (`T0`, `T1`) are used for each oscillatory state, corresponding to biological understanding of duration and nature of these rhythms. Overall, the code is designed to emulate and study the function of thalamic network oscillations, providing insights into the roles and interactions of various neuron types within the thalamus during these different states of brain activity.